Starting phenix.real_space_refine on Wed Feb 4 10:20:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mh8_48267/02_2026/9mh8_48267.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mh8_48267/02_2026/9mh8_48267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mh8_48267/02_2026/9mh8_48267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mh8_48267/02_2026/9mh8_48267.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mh8_48267/02_2026/9mh8_48267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mh8_48267/02_2026/9mh8_48267.map" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.008 sd= 0.083 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 50 5.16 5 C 6376 2.51 5 N 1590 2.21 5 O 1765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9781 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2533 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 10, 'TRANS': 316} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'HIS:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2405 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 10, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 8, 'GLN:plan1': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 100 Chain: "C" Number of atoms: 2387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2387 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 10, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 4, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 93 Chain: "D" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2456 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 7, 'TYR:plan': 2, 'ARG:plan': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 76 Time building chain proxies: 1.89, per 1000 atoms: 0.19 Number of scatterers: 9781 At special positions: 0 Unit cell: (89.796, 87.658, 132.556, 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 50 16.00 O 1765 8.00 N 1590 7.00 C 6376 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: 0.54 Conformation dependent library (CDL) restraints added in 308.9 milliseconds 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 19 sheets defined 37.0% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 73 through 91 removed outlier: 3.933A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 118 removed outlier: 3.581A pdb=" N LEU A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 153 Processing helix chain 'A' and resid 166 through 197 removed outlier: 3.639A pdb=" N ILE A 170 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS A 194 " --> pdb=" O CYS A 190 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE A 195 " --> pdb=" O MET A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 removed outlier: 4.054A pdb=" N GLU A 293 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.552A pdb=" N GLU A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'B' and resid 76 through 91 removed outlier: 3.772A pdb=" N TRP B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 121 removed outlier: 4.007A pdb=" N LEU B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR B 102 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 153 Processing helix chain 'B' and resid 166 through 196 Processing helix chain 'B' and resid 289 through 294 removed outlier: 4.242A pdb=" N GLU B 293 " --> pdb=" O PRO B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 4.649A pdb=" N LYS B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 356 Processing helix chain 'B' and resid 368 through 381 Processing helix chain 'C' and resid 78 through 90 Processing helix chain 'C' and resid 94 through 121 Processing helix chain 'C' and resid 140 through 153 Processing helix chain 'C' and resid 166 through 192 Processing helix chain 'C' and resid 289 through 294 removed outlier: 4.277A pdb=" N GLU C 293 " --> pdb=" O PRO C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 removed outlier: 4.406A pdb=" N LYS C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 357 removed outlier: 4.508A pdb=" N HIS C 357 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 381 Processing helix chain 'D' and resid 75 through 121 removed outlier: 3.717A pdb=" N LEU D 89 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N PHE D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N MET D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL D 101 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 117 " --> pdb=" O TRP D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 142 through 153 removed outlier: 3.707A pdb=" N THR D 153 " --> pdb=" O ILE D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 196 removed outlier: 3.745A pdb=" N ILE D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 293 removed outlier: 4.218A pdb=" N GLU D 293 " --> pdb=" O PRO D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 303 removed outlier: 4.342A pdb=" N GLU D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 356 Processing helix chain 'D' and resid 368 through 381 Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 201 removed outlier: 3.588A pdb=" N GLN A 322 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N MET A 313 " --> pdb=" O GLU A 236 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLU A 236 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ALA A 241 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LYS A 247 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 201 removed outlier: 3.588A pdb=" N GLN A 322 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N MET A 313 " --> pdb=" O GLU A 236 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLU A 236 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 207 Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 207 Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 345 Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 201 removed outlier: 6.741A pdb=" N LYS B 200 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N ARG B 324 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS B 321 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY B 312 " --> pdb=" O CYS B 321 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET B 313 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLU B 236 " --> pdb=" O MET B 313 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LYS B 247 " --> pdb=" O PRO B 256 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 199 through 201 removed outlier: 6.741A pdb=" N LYS B 200 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N ARG B 324 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS B 321 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY B 312 " --> pdb=" O CYS B 321 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET B 313 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLU B 236 " --> pdb=" O MET B 313 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 279 through 284 Processing sheet with id=AA9, first strand: chain 'B' and resid 336 through 338 Processing sheet with id=AB1, first strand: chain 'B' and resid 342 through 345 Processing sheet with id=AB2, first strand: chain 'C' and resid 199 through 200 removed outlier: 4.027A pdb=" N GLN C 322 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LYS C 247 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 279 through 284 removed outlier: 6.622A pdb=" N ALA C 211 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 336 through 338 Processing sheet with id=AB5, first strand: chain 'C' and resid 342 through 344 Processing sheet with id=AB6, first strand: chain 'D' and resid 199 through 200 removed outlier: 6.808A pdb=" N LYS D 200 " --> pdb=" O GLN D 322 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N ARG D 324 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU D 236 " --> pdb=" O MET D 313 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA D 241 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYS D 247 " --> pdb=" O PRO D 256 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 199 through 200 removed outlier: 6.808A pdb=" N LYS D 200 " --> pdb=" O GLN D 322 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N ARG D 324 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU D 236 " --> pdb=" O MET D 313 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 279 through 284 Processing sheet with id=AB9, first strand: chain 'D' and resid 336 through 338 Processing sheet with id=AC1, first strand: chain 'D' and resid 342 through 344 539 hydrogen bonds defined for protein. 1524 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: 1.23 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2767 1.33 - 1.46: 2215 1.46 - 1.58: 4952 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 10013 Sorted by residual: bond pdb=" N PHE A 109 " pdb=" CA PHE A 109 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 5.98e+00 bond pdb=" N PHE A 108 " pdb=" CA PHE A 108 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.41e+00 bond pdb=" N LEU A 107 " pdb=" CA LEU A 107 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.96e+00 bond pdb=" N TRP A 106 " pdb=" CA TRP A 106 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.76e+00 bond pdb=" N THR A 105 " pdb=" CA THR A 105 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.78e+00 ... (remaining 10008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 13521 2.52 - 5.03: 102 5.03 - 7.55: 14 7.55 - 10.06: 4 10.06 - 12.58: 3 Bond angle restraints: 13644 Sorted by residual: angle pdb=" C SER A 363 " pdb=" N THR A 364 " pdb=" CA THR A 364 " ideal model delta sigma weight residual 121.80 132.36 -10.56 2.44e+00 1.68e-01 1.87e+01 angle pdb=" CB MET C 215 " pdb=" CG MET C 215 " pdb=" SD MET C 215 " ideal model delta sigma weight residual 112.70 125.28 -12.58 3.00e+00 1.11e-01 1.76e+01 angle pdb=" N VAL D 264 " pdb=" CA VAL D 264 " pdb=" C VAL D 264 " ideal model delta sigma weight residual 111.91 108.43 3.48 8.90e-01 1.26e+00 1.53e+01 angle pdb=" CA TRP D 91 " pdb=" CB TRP D 91 " pdb=" CG TRP D 91 " ideal model delta sigma weight residual 113.60 121.00 -7.40 1.90e+00 2.77e-01 1.52e+01 angle pdb=" CB MET C 100 " pdb=" CG MET C 100 " pdb=" SD MET C 100 " ideal model delta sigma weight residual 112.70 123.95 -11.25 3.00e+00 1.11e-01 1.41e+01 ... (remaining 13639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5108 17.90 - 35.79: 545 35.79 - 53.69: 153 53.69 - 71.59: 14 71.59 - 89.48: 11 Dihedral angle restraints: 5831 sinusoidal: 2103 harmonic: 3728 Sorted by residual: dihedral pdb=" CA TYR C 58 " pdb=" C TYR C 58 " pdb=" N VAL C 59 " pdb=" CA VAL C 59 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ALA C 237 " pdb=" C ALA C 237 " pdb=" N SER C 238 " pdb=" CA SER C 238 " ideal model delta harmonic sigma weight residual 180.00 163.27 16.73 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA ASP A 164 " pdb=" CB ASP A 164 " pdb=" CG ASP A 164 " pdb=" OD1 ASP A 164 " ideal model delta sinusoidal sigma weight residual -30.00 -85.87 55.87 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 5828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1074 0.034 - 0.068: 358 0.068 - 0.103: 121 0.103 - 0.137: 44 0.137 - 0.171: 6 Chirality restraints: 1603 Sorted by residual: chirality pdb=" CB ILE D 255 " pdb=" CA ILE D 255 " pdb=" CG1 ILE D 255 " pdb=" CG2 ILE D 255 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA THR A 364 " pdb=" N THR A 364 " pdb=" C THR A 364 " pdb=" CB THR A 364 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA PHE A 108 " pdb=" N PHE A 108 " pdb=" C PHE A 108 " pdb=" CB PHE A 108 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 1600 not shown) Planarity restraints: 1690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 91 " -0.014 2.00e-02 2.50e+03 1.70e-02 7.22e+00 pdb=" CG TRP D 91 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 91 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 91 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 91 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 91 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 91 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 91 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 91 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 91 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 98 " -0.015 2.00e-02 2.50e+03 1.52e-02 4.06e+00 pdb=" CG PHE A 98 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 98 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 98 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 98 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 98 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 98 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 98 " 0.008 2.00e-02 2.50e+03 1.22e-02 2.60e+00 pdb=" CG PHE D 98 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE D 98 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE D 98 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 98 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 98 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE D 98 " -0.003 2.00e-02 2.50e+03 ... (remaining 1687 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 568 2.73 - 3.27: 10116 3.27 - 3.81: 16249 3.81 - 4.36: 17742 4.36 - 4.90: 31518 Nonbonded interactions: 76193 Sorted by model distance: nonbonded pdb=" O SER A 363 " pdb=" OG1 THR A 364 " model vdw 2.184 3.040 nonbonded pdb=" NZ LYS B 219 " pdb=" OE2 GLU B 284 " model vdw 2.197 3.120 nonbonded pdb=" O PHE B 192 " pdb=" OG SER B 196 " model vdw 2.210 3.040 nonbonded pdb=" OG SER A 368 " pdb=" OE1 GLU A 371 " model vdw 2.212 3.040 nonbonded pdb=" O VAL A 99 " pdb=" OG1 THR A 103 " model vdw 2.216 3.040 ... (remaining 76188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 55 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 through 64 or (resid 77 through 90 and (na \ me N or name CA or name C or name O or name CB )) or resid 91 through 190 or (re \ sid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 th \ rough 193 or (resid 194 and (name N or name CA or name C or name O or name CB )) \ or resid 195 through 196 or (resid 197 and (name N or name CA or name C or name \ O or name CB )) or resid 198 or (resid 199 through 203 and (name N or name CA o \ r name C or name O or name CB )) or resid 204 through 229 or (resid 230 through \ 231 and (name N or name CA or name C or name O or name CB )) or resid 232 throug \ h 250 or (resid 251 and (name N or name CA or name C or name O or name CB )) or \ resid 252 or (resid 253 and (name N or name CA or name C or name O or name CB )) \ or resid 254 through 286 or (resid 287 through 288 and (name N or name CA or na \ me C or name O or name CB )) or resid 289 through 312 or (resid 313 and (name N \ or name CA or name C or name O or name CB )) or resid 314 through 370 or (resid \ 371 and (name N or name CA or name C or name O or name CB )) or resid 372 throug \ h 374 or (resid 375 through 381 and (name N or name CA or name C or name O or na \ me CB )))) selection = (chain 'B' and (resid 55 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 through 61 or (resid 62 and (name N or nam \ e CA or name C or name O or name CB )) or resid 63 or (resid 64 and (name N or n \ ame CA or name C or name O or name CB )) or resid 77 through 121 or (resid 122 a \ nd (name N or name CA or name C or name O or name CB )) or resid 123 through 193 \ or (resid 194 and (name N or name CA or name C or name O or name CB )) or resid \ 195 or (resid 196 through 197 and (name N or name CA or name C or name O or nam \ e CB )) or resid 198 through 200 or (resid 201 through 203 and (name N or name C \ A or name C or name O or name CB )) or resid 204 through 216 or (resid 217 and ( \ name N or name CA or name C or name O or name CB )) or resid 218 through 230 or \ (resid 231 and (name N or name CA or name C or name O or name CB )) or resid 232 \ through 250 or (resid 251 and (name N or name CA or name C or name O or name CB \ )) or resid 252 through 302 or (resid 303 and (name N or name CA or name C or n \ ame O or name CB )) or resid 304 through 374 or (resid 375 through 381 and (name \ N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 55 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB )) or resid 123 through 190 or (resid 191 and (name N o \ r name CA or name C or name O or name CB )) or resid 192 through 195 or (resid 1 \ 96 through 197 and (name N or name CA or name C or name O or name CB )) or resid \ 198 through 216 or (resid 217 and (name N or name CA or name C or name O or nam \ e CB )) or resid 218 through 252 or (resid 253 and (name N or name CA or name C \ or name O or name CB )) or resid 254 through 286 or (resid 287 through 288 and ( \ name N or name CA or name C or name O or name CB )) or resid 289 through 312 or \ (resid 313 and (name N or name CA or name C or name O or name CB )) or resid 314 \ through 353 or (resid 354 and (name N or name CA or name C or name O or name CB \ )) or resid 355 through 370 or (resid 371 and (name N or name CA or name C or n \ ame O or name CB )) or resid 372 through 381)) selection = (chain 'D' and (resid 55 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 or (resid 61 through 62 and (name N or nam \ e CA or name C or name O or name CB )) or resid 63 through 64 or (resid 77 throu \ gh 90 and (name N or name CA or name C or name O or name CB )) or resid 91 throu \ gh 121 or (resid 122 and (name N or name CA or name C or name O or name CB )) or \ resid 123 through 193 or (resid 194 and (name N or name CA or name C or name O \ or name CB )) or resid 195 through 196 or (resid 197 and (name N or name CA or n \ ame C or name O or name CB )) or resid 198 or (resid 199 through 203 and (name N \ or name CA or name C or name O or name CB )) or resid 204 through 216 or (resid \ 217 and (name N or name CA or name C or name O or name CB )) or resid 218 throu \ gh 229 or (resid 230 through 231 and (name N or name CA or name C or name O or n \ ame CB )) or resid 232 through 250 or (resid 251 and (name N or name CA or name \ C or name O or name CB )) or resid 252 or (resid 253 and (name N or name CA or n \ ame C or name O or name CB )) or resid 254 through 286 or (resid 287 through 288 \ and (name N or name CA or name C or name O or name CB )) or resid 289 through 3 \ 12 or (resid 313 and (name N or name CA or name C or name O or name CB )) or res \ id 314 through 353 or (resid 354 and (name N or name CA or name C or name O or n \ ame CB )) or resid 355 through 370 or (resid 371 and (name N or name CA or name \ C or name O or name CB )) or resid 372 through 374 or (resid 375 through 381 and \ (name N or name CA or name C or name O or name CB )))) } 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: 1.040 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.200 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 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 : 0.003 0.032 10013 Z= 0.158 Angle : 0.621 12.577 13644 Z= 0.331 Chirality : 0.042 0.171 1603 Planarity : 0.003 0.036 1690 Dihedral : 16.180 89.481 3423 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.35 % Favored : 95.49 % Rotamer: Outliers : 0.40 % Allowed : 27.74 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.24), residues: 1263 helix: 2.64 (0.25), residues: 388 sheet: 0.80 (0.35), residues: 215 loop : -0.52 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 225 TYR 0.015 0.001 TYR A 360 PHE 0.035 0.001 PHE A 98 TRP 0.046 0.001 TRP D 91 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00320 (10013) covalent geometry : angle 0.62050 (13644) hydrogen bonds : bond 0.12246 ( 489) hydrogen bonds : angle 5.56940 ( 1524) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 215 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 VAL cc_start: 0.5516 (m) cc_final: 0.5305 (p) REVERT: A 91 TRP cc_start: 0.6362 (m100) cc_final: 0.5897 (m100) REVERT: A 107 LEU cc_start: 0.8598 (tp) cc_final: 0.8372 (mt) REVERT: A 131 TRP cc_start: 0.7036 (t-100) cc_final: 0.6755 (t-100) REVERT: A 192 PHE cc_start: 0.8369 (t80) cc_final: 0.8146 (t80) REVERT: B 165 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7459 (mmmt) REVERT: B 187 MET cc_start: 0.6365 (tpp) cc_final: 0.6158 (tpp) REVERT: B 201 ARG cc_start: 0.7490 (ttm110) cc_final: 0.7275 (ttm170) REVERT: C 111 MET cc_start: 0.6601 (tpt) cc_final: 0.6281 (tpt) REVERT: C 186 PHE cc_start: 0.7387 (t80) cc_final: 0.7072 (t80) REVERT: C 191 MET cc_start: 0.6403 (mmp) cc_final: 0.6097 (mmp) REVERT: C 222 LEU cc_start: 0.5405 (OUTLIER) cc_final: 0.5142 (tt) REVERT: C 321 CYS cc_start: 0.8246 (m) cc_final: 0.7926 (p) REVERT: C 361 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7501 (tm-30) REVERT: D 248 GLN cc_start: 0.8631 (tt0) cc_final: 0.8370 (tt0) outliers start: 4 outliers final: 1 residues processed: 218 average time/residue: 0.0744 time to fit residues: 23.1539 Evaluate side-chains 186 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain C residue 222 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 123 optimal weight: 0.4980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN C 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.169368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.124436 restraints weight = 13457.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125110 restraints weight = 10511.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127656 restraints weight = 8771.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128234 restraints weight = 7350.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128629 restraints weight = 7257.426| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10013 Z= 0.151 Angle : 0.581 13.013 13644 Z= 0.305 Chirality : 0.044 0.151 1603 Planarity : 0.004 0.036 1690 Dihedral : 4.429 51.735 1368 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.12 % Favored : 95.72 % Rotamer: Outliers : 4.79 % Allowed : 25.35 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.24), residues: 1263 helix: 2.80 (0.24), residues: 388 sheet: 0.51 (0.34), residues: 229 loop : -0.51 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 60 TYR 0.014 0.001 TYR A 360 PHE 0.023 0.001 PHE D 93 TRP 0.033 0.002 TRP D 91 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00348 (10013) covalent geometry : angle 0.58107 (13644) hydrogen bonds : bond 0.03550 ( 489) hydrogen bonds : angle 4.34758 ( 1524) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 91 TRP cc_start: 0.6241 (m100) cc_final: 0.5952 (m100) REVERT: A 92 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8252 (t80) REVERT: A 163 THR cc_start: 0.7669 (m) cc_final: 0.7374 (p) REVERT: A 191 MET cc_start: 0.8184 (tmm) cc_final: 0.7963 (tmm) REVERT: B 165 LYS cc_start: 0.8517 (mmmt) cc_final: 0.8192 (mmmt) REVERT: B 187 MET cc_start: 0.7458 (tpp) cc_final: 0.7162 (tpp) REVERT: B 298 GLN cc_start: 0.8645 (tt0) cc_final: 0.8342 (tt0) REVERT: C 111 MET cc_start: 0.6324 (tpt) cc_final: 0.6026 (tpt) REVERT: C 120 ARG cc_start: 0.7571 (mtp180) cc_final: 0.7329 (ttt180) REVERT: C 186 PHE cc_start: 0.8302 (t80) cc_final: 0.7910 (t80) REVERT: C 240 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7799 (mtp180) REVERT: C 298 GLN cc_start: 0.8046 (tp40) cc_final: 0.7735 (tp40) REVERT: C 361 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7358 (tm-30) outliers start: 48 outliers final: 26 residues processed: 224 average time/residue: 0.0758 time to fit residues: 24.4843 Evaluate side-chains 195 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 122 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 83 optimal weight: 0.0370 chunk 62 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN ** C 287 GLN ** 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 = 0.4187 r_free = 0.4187 target = 0.172989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.129015 restraints weight = 13529.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.131239 restraints weight = 11163.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.133456 restraints weight = 9214.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.133777 restraints weight = 7403.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.134049 restraints weight = 7393.899| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10013 Z= 0.238 Angle : 0.652 12.591 13644 Z= 0.342 Chirality : 0.046 0.155 1603 Planarity : 0.004 0.038 1690 Dihedral : 4.651 46.483 1366 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.54 % Favored : 94.30 % Rotamer: Outliers : 7.29 % Allowed : 24.55 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.23), residues: 1263 helix: 2.48 (0.24), residues: 393 sheet: 0.23 (0.35), residues: 217 loop : -0.73 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 225 TYR 0.012 0.002 TYR D 349 PHE 0.022 0.002 PHE D 93 TRP 0.029 0.002 TRP D 91 HIS 0.004 0.001 HIS D 357 Details of bonding type rmsd covalent geometry : bond 0.00562 (10013) covalent geometry : angle 0.65232 (13644) hydrogen bonds : bond 0.03785 ( 489) hydrogen bonds : angle 4.47209 ( 1524) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 174 time to evaluate : 0.315 Fit side-chains REVERT: A 91 TRP cc_start: 0.6285 (m100) cc_final: 0.6081 (m100) REVERT: A 152 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: A 163 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7793 (p) REVERT: B 165 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8235 (mmmt) REVERT: B 222 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6835 (tt) REVERT: C 111 MET cc_start: 0.6294 (tpt) cc_final: 0.5999 (tpt) REVERT: C 186 PHE cc_start: 0.8271 (t80) cc_final: 0.7888 (t80) REVERT: C 240 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7745 (mtp180) REVERT: C 298 GLN cc_start: 0.8093 (tp40) cc_final: 0.7769 (tp40) REVERT: D 98 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.6636 (t80) REVERT: D 132 THR cc_start: 0.8311 (m) cc_final: 0.7986 (p) REVERT: D 253 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7620 (mt-10) outliers start: 73 outliers final: 48 residues processed: 229 average time/residue: 0.0791 time to fit residues: 26.5124 Evaluate side-chains 218 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 104 optimal weight: 0.0040 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 231 ASN C 287 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.174914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.131837 restraints weight = 13346.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133448 restraints weight = 10593.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.136042 restraints weight = 8678.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136350 restraints weight = 7191.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.136738 restraints weight = 7150.171| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10013 Z= 0.135 Angle : 0.575 12.430 13644 Z= 0.299 Chirality : 0.044 0.245 1603 Planarity : 0.004 0.037 1690 Dihedral : 4.272 34.685 1366 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.43 % Favored : 95.49 % Rotamer: Outliers : 6.19 % Allowed : 25.75 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.24), residues: 1263 helix: 2.68 (0.24), residues: 387 sheet: 0.35 (0.35), residues: 221 loop : -0.59 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 201 TYR 0.010 0.001 TYR D 102 PHE 0.028 0.001 PHE A 98 TRP 0.027 0.001 TRP D 91 HIS 0.002 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00309 (10013) covalent geometry : angle 0.57495 (13644) hydrogen bonds : bond 0.03354 ( 489) hydrogen bonds : angle 4.24410 ( 1524) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 169 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 91 TRP cc_start: 0.6299 (m100) cc_final: 0.6072 (m100) REVERT: A 123 MET cc_start: 0.8543 (mpp) cc_final: 0.7938 (mpp) REVERT: A 152 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: B 165 LYS cc_start: 0.8482 (mmmt) cc_final: 0.8243 (mmmt) REVERT: B 187 MET cc_start: 0.7874 (tpp) cc_final: 0.7370 (tpp) REVERT: C 98 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.6174 (t80) REVERT: C 111 MET cc_start: 0.6184 (tpt) cc_final: 0.5874 (tpt) REVERT: C 186 PHE cc_start: 0.8294 (t80) cc_final: 0.8002 (t80) REVERT: C 240 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7849 (mtp180) REVERT: C 298 GLN cc_start: 0.7903 (tp40) cc_final: 0.7519 (tp40) REVERT: D 98 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6797 (t80) REVERT: D 107 LEU cc_start: 0.8489 (tp) cc_final: 0.8238 (tp) REVERT: D 132 THR cc_start: 0.8352 (m) cc_final: 0.7982 (p) outliers start: 62 outliers final: 41 residues processed: 218 average time/residue: 0.0827 time to fit residues: 26.3410 Evaluate side-chains 209 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN D 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.166318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118186 restraints weight = 13640.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.122027 restraints weight = 9697.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124529 restraints weight = 7908.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125862 restraints weight = 6963.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127238 restraints weight = 6445.990| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10013 Z= 0.135 Angle : 0.590 12.492 13644 Z= 0.302 Chirality : 0.044 0.236 1603 Planarity : 0.004 0.036 1690 Dihedral : 4.177 32.061 1366 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.57 % Rotamer: Outliers : 6.19 % Allowed : 25.75 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1263 helix: 2.74 (0.24), residues: 384 sheet: 0.32 (0.35), residues: 232 loop : -0.48 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 201 TYR 0.010 0.001 TYR D 102 PHE 0.034 0.001 PHE A 98 TRP 0.027 0.001 TRP D 91 HIS 0.002 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00311 (10013) covalent geometry : angle 0.58967 (13644) hydrogen bonds : bond 0.03281 ( 489) hydrogen bonds : angle 4.15955 ( 1524) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 169 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 91 TRP cc_start: 0.6276 (m100) cc_final: 0.6016 (m100) REVERT: A 123 MET cc_start: 0.8565 (mpp) cc_final: 0.8074 (mpp) REVERT: A 152 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: A 163 THR cc_start: 0.7977 (m) cc_final: 0.7596 (p) REVERT: A 236 GLU cc_start: 0.8527 (pm20) cc_final: 0.8313 (pm20) REVERT: B 165 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8194 (mmmt) REVERT: B 187 MET cc_start: 0.7939 (tpp) cc_final: 0.7715 (tpp) REVERT: B 222 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6374 (tt) REVERT: B 298 GLN cc_start: 0.8610 (mt0) cc_final: 0.8039 (tt0) REVERT: C 111 MET cc_start: 0.6567 (tpt) cc_final: 0.6223 (tpt) REVERT: C 186 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7561 (t80) REVERT: C 240 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7738 (mtp180) REVERT: C 298 GLN cc_start: 0.7974 (tp40) cc_final: 0.7594 (tp40) REVERT: D 107 LEU cc_start: 0.8510 (tp) cc_final: 0.8287 (tp) REVERT: D 132 THR cc_start: 0.8294 (m) cc_final: 0.7977 (p) REVERT: D 287 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7789 (mm-40) outliers start: 62 outliers final: 44 residues processed: 216 average time/residue: 0.0660 time to fit residues: 21.3278 Evaluate side-chains 216 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 66 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 104 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN C 322 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.165542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117790 restraints weight = 13502.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121602 restraints weight = 9607.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.124072 restraints weight = 7811.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.125818 restraints weight = 6865.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126679 restraints weight = 6301.095| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10013 Z= 0.142 Angle : 0.587 12.450 13644 Z= 0.304 Chirality : 0.044 0.229 1603 Planarity : 0.004 0.037 1690 Dihedral : 4.086 17.809 1365 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.59 % Favored : 95.33 % Rotamer: Outliers : 5.69 % Allowed : 26.45 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.24), residues: 1263 helix: 2.64 (0.24), residues: 389 sheet: 0.33 (0.34), residues: 232 loop : -0.48 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 201 TYR 0.010 0.001 TYR D 157 PHE 0.028 0.001 PHE A 98 TRP 0.026 0.001 TRP D 91 HIS 0.002 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00329 (10013) covalent geometry : angle 0.58684 (13644) hydrogen bonds : bond 0.03284 ( 489) hydrogen bonds : angle 4.15307 ( 1524) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 170 time to evaluate : 0.255 Fit side-chains REVERT: A 91 TRP cc_start: 0.6310 (m100) cc_final: 0.6050 (m100) REVERT: A 123 MET cc_start: 0.8451 (mpp) cc_final: 0.7919 (mpp) REVERT: A 152 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: A 163 THR cc_start: 0.8010 (m) cc_final: 0.7630 (p) REVERT: A 236 GLU cc_start: 0.8482 (pm20) cc_final: 0.8207 (pm20) REVERT: B 165 LYS cc_start: 0.8472 (mmmt) cc_final: 0.8156 (mmmt) REVERT: B 222 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6369 (tt) REVERT: B 298 GLN cc_start: 0.8564 (mt0) cc_final: 0.7960 (tt0) REVERT: B 370 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8397 (ttmm) REVERT: C 111 MET cc_start: 0.6595 (tpt) cc_final: 0.6239 (tpt) REVERT: C 240 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7701 (mtp180) REVERT: C 292 TRP cc_start: 0.9098 (t-100) cc_final: 0.8634 (t-100) REVERT: C 298 GLN cc_start: 0.7991 (tp40) cc_final: 0.7639 (tp40) REVERT: D 107 LEU cc_start: 0.8537 (tp) cc_final: 0.8317 (tp) REVERT: D 132 THR cc_start: 0.8308 (m) cc_final: 0.8006 (p) REVERT: D 187 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7399 (mmm) REVERT: D 287 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7920 (mm-40) outliers start: 57 outliers final: 48 residues processed: 211 average time/residue: 0.0714 time to fit residues: 22.3045 Evaluate side-chains 220 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 322 GLN Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 119 optimal weight: 0.9990 chunk 45 optimal weight: 0.0020 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 40 optimal weight: 0.0470 chunk 74 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 33 optimal weight: 20.0000 chunk 115 optimal weight: 0.9980 overall best weight: 0.5086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.166985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119722 restraints weight = 13463.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123682 restraints weight = 9445.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.126331 restraints weight = 7608.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.127361 restraints weight = 6634.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128179 restraints weight = 6187.294| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10013 Z= 0.118 Angle : 0.579 12.445 13644 Z= 0.297 Chirality : 0.043 0.226 1603 Planarity : 0.003 0.036 1690 Dihedral : 4.001 17.829 1365 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.57 % Rotamer: Outliers : 5.09 % Allowed : 27.05 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.24), residues: 1263 helix: 2.55 (0.25), residues: 391 sheet: 0.40 (0.34), residues: 232 loop : -0.42 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 201 TYR 0.012 0.001 TYR D 102 PHE 0.022 0.001 PHE D 93 TRP 0.026 0.001 TRP D 91 HIS 0.003 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00266 (10013) covalent geometry : angle 0.57893 (13644) hydrogen bonds : bond 0.03184 ( 489) hydrogen bonds : angle 4.08357 ( 1524) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 169 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 91 TRP cc_start: 0.6282 (m100) cc_final: 0.6017 (m100) REVERT: A 100 MET cc_start: 0.7641 (mtm) cc_final: 0.6751 (mmp) REVERT: A 152 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.6813 (tm-30) REVERT: A 163 THR cc_start: 0.7946 (m) cc_final: 0.7582 (p) REVERT: A 236 GLU cc_start: 0.8455 (pm20) cc_final: 0.8186 (pm20) REVERT: B 165 LYS cc_start: 0.8474 (mmmt) cc_final: 0.8144 (mmmt) REVERT: B 187 MET cc_start: 0.7603 (tpp) cc_final: 0.7269 (tpp) REVERT: B 370 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8472 (ttmm) REVERT: C 111 MET cc_start: 0.6558 (tpt) cc_final: 0.6209 (tpt) REVERT: C 240 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7475 (mtp180) REVERT: C 298 GLN cc_start: 0.7978 (tp40) cc_final: 0.7637 (tp40) REVERT: D 107 LEU cc_start: 0.8546 (tp) cc_final: 0.8321 (tp) REVERT: D 132 THR cc_start: 0.8289 (m) cc_final: 0.7993 (p) REVERT: D 187 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7368 (mmm) REVERT: D 287 GLN cc_start: 0.8318 (mm-40) cc_final: 0.7931 (mm-40) outliers start: 51 outliers final: 42 residues processed: 206 average time/residue: 0.0783 time to fit residues: 23.7397 Evaluate side-chains 208 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.174621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.134333 restraints weight = 13473.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.134838 restraints weight = 12629.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136845 restraints weight = 10905.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.137316 restraints weight = 8459.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.137609 restraints weight = 8177.493| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10013 Z= 0.198 Angle : 0.630 12.358 13644 Z= 0.324 Chirality : 0.045 0.220 1603 Planarity : 0.004 0.038 1690 Dihedral : 4.240 17.556 1365 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 6.29 % Allowed : 26.15 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.24), residues: 1263 helix: 2.53 (0.25), residues: 390 sheet: 0.22 (0.34), residues: 232 loop : -0.53 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 201 TYR 0.015 0.001 TYR D 157 PHE 0.024 0.002 PHE B 186 TRP 0.027 0.001 TRP D 91 HIS 0.003 0.001 HIS D 357 Details of bonding type rmsd covalent geometry : bond 0.00472 (10013) covalent geometry : angle 0.63046 (13644) hydrogen bonds : bond 0.03423 ( 489) hydrogen bonds : angle 4.23002 ( 1524) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 168 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 91 TRP cc_start: 0.6374 (m100) cc_final: 0.6153 (m100) REVERT: A 100 MET cc_start: 0.7599 (mtm) cc_final: 0.6849 (mmp) REVERT: A 152 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: A 371 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7307 (pt0) REVERT: B 187 MET cc_start: 0.7854 (tpp) cc_final: 0.7599 (tpp) REVERT: B 222 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6772 (tt) REVERT: B 223 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7881 (ptp) REVERT: B 240 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7425 (mtm110) REVERT: C 111 MET cc_start: 0.6323 (tpt) cc_final: 0.6011 (tpt) REVERT: C 186 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7656 (t80) REVERT: C 240 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7805 (mtp180) REVERT: C 292 TRP cc_start: 0.8960 (t-100) cc_final: 0.8527 (t-100) REVERT: C 298 GLN cc_start: 0.7874 (tp40) cc_final: 0.7515 (tp40) REVERT: D 98 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6697 (t80) REVERT: D 107 LEU cc_start: 0.8585 (tp) cc_final: 0.8351 (tp) REVERT: D 287 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7753 (mm-40) outliers start: 63 outliers final: 51 residues processed: 212 average time/residue: 0.0689 time to fit residues: 21.2898 Evaluate side-chains 220 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 162 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 43 optimal weight: 0.5980 chunk 59 optimal weight: 0.0670 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN B 283 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.173483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.132225 restraints weight = 13463.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132409 restraints weight = 12279.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.134708 restraints weight = 10573.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.135052 restraints weight = 8753.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.135314 restraints weight = 8352.664| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10013 Z= 0.201 Angle : 0.651 12.335 13644 Z= 0.334 Chirality : 0.045 0.214 1603 Planarity : 0.004 0.039 1690 Dihedral : 4.354 19.387 1365 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 6.09 % Allowed : 25.95 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.24), residues: 1263 helix: 2.45 (0.25), residues: 392 sheet: 0.11 (0.35), residues: 222 loop : -0.60 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 201 TYR 0.017 0.001 TYR D 157 PHE 0.022 0.002 PHE D 93 TRP 0.028 0.002 TRP A 114 HIS 0.003 0.001 HIS D 357 Details of bonding type rmsd covalent geometry : bond 0.00478 (10013) covalent geometry : angle 0.65099 (13644) hydrogen bonds : bond 0.03450 ( 489) hydrogen bonds : angle 4.29151 ( 1524) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 162 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.7604 (mtm) cc_final: 0.6844 (mmp) REVERT: A 123 MET cc_start: 0.8251 (mpp) cc_final: 0.7369 (mpp) REVERT: A 152 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: A 292 TRP cc_start: 0.8727 (t-100) cc_final: 0.8276 (t-100) REVERT: A 371 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7301 (pt0) REVERT: B 187 MET cc_start: 0.7842 (tpp) cc_final: 0.7640 (tpp) REVERT: B 201 ARG cc_start: 0.7040 (ttm110) cc_final: 0.6816 (ttm110) REVERT: B 222 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6802 (tt) REVERT: B 223 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7889 (ptp) REVERT: B 240 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7431 (mtm110) REVERT: C 111 MET cc_start: 0.6336 (tpt) cc_final: 0.6028 (tpt) REVERT: C 240 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7799 (mtp180) REVERT: C 292 TRP cc_start: 0.8984 (t-100) cc_final: 0.8586 (t-100) REVERT: C 298 GLN cc_start: 0.7876 (tp40) cc_final: 0.7525 (tp40) REVERT: D 98 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6655 (t80) REVERT: D 107 LEU cc_start: 0.8602 (tp) cc_final: 0.8369 (tp) REVERT: D 287 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7721 (mm-40) outliers start: 61 outliers final: 50 residues processed: 206 average time/residue: 0.0751 time to fit residues: 22.5317 Evaluate side-chains 217 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 161 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN B 283 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.175978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.134048 restraints weight = 13434.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.135372 restraints weight = 12753.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.137647 restraints weight = 10376.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.138227 restraints weight = 8318.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138386 restraints weight = 8153.016| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10013 Z= 0.149 Angle : 0.618 12.671 13644 Z= 0.316 Chirality : 0.044 0.208 1603 Planarity : 0.004 0.037 1690 Dihedral : 4.210 19.484 1365 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 5.69 % Allowed : 26.45 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.24), residues: 1263 helix: 2.50 (0.25), residues: 391 sheet: 0.17 (0.35), residues: 222 loop : -0.56 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 201 TYR 0.016 0.001 TYR D 157 PHE 0.023 0.001 PHE D 93 TRP 0.030 0.002 TRP A 114 HIS 0.002 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00348 (10013) covalent geometry : angle 0.61769 (13644) hydrogen bonds : bond 0.03282 ( 489) hydrogen bonds : angle 4.21552 ( 1524) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 166 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 TRP cc_start: 0.6612 (m100) cc_final: 0.6243 (m100) REVERT: A 100 MET cc_start: 0.7564 (mtm) cc_final: 0.6800 (mmp) REVERT: A 152 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: A 223 MET cc_start: 0.8150 (ptp) cc_final: 0.7575 (ptt) REVERT: A 292 TRP cc_start: 0.8706 (t-100) cc_final: 0.8277 (t-100) REVERT: B 187 MET cc_start: 0.7851 (tpp) cc_final: 0.7622 (tpp) REVERT: B 370 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8324 (ttmm) REVERT: C 111 MET cc_start: 0.6301 (tpt) cc_final: 0.5986 (tpt) REVERT: C 240 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7810 (mtp180) REVERT: C 292 TRP cc_start: 0.8975 (t-100) cc_final: 0.8583 (t-100) REVERT: C 298 GLN cc_start: 0.7807 (tp40) cc_final: 0.7440 (tp40) REVERT: D 98 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.6584 (t80) REVERT: D 107 LEU cc_start: 0.8603 (tp) cc_final: 0.8373 (tp) REVERT: D 287 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7680 (mm-40) outliers start: 57 outliers final: 52 residues processed: 206 average time/residue: 0.0710 time to fit residues: 21.6551 Evaluate side-chains 215 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 160 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 11 optimal weight: 0.0870 chunk 2 optimal weight: 9.9990 chunk 109 optimal weight: 0.4980 chunk 123 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 57 optimal weight: 0.0370 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 0.0770 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.180624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.137905 restraints weight = 13472.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140073 restraints weight = 11584.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141808 restraints weight = 9828.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.142268 restraints weight = 8795.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.142689 restraints weight = 8385.925| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10013 Z= 0.110 Angle : 0.603 12.604 13644 Z= 0.305 Chirality : 0.043 0.202 1603 Planarity : 0.003 0.037 1690 Dihedral : 3.985 17.774 1365 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.88 % Favored : 96.04 % Rotamer: Outliers : 4.79 % Allowed : 27.64 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1263 helix: 2.53 (0.25), residues: 393 sheet: 0.37 (0.34), residues: 233 loop : -0.41 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 201 TYR 0.011 0.001 TYR D 102 PHE 0.028 0.001 PHE A 186 TRP 0.033 0.002 TRP A 114 HIS 0.003 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00240 (10013) covalent geometry : angle 0.60313 (13644) hydrogen bonds : bond 0.03049 ( 489) hydrogen bonds : angle 4.06305 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1373.11 seconds wall clock time: 24 minutes 28.69 seconds (1468.69 seconds total)