Starting phenix.real_space_refine on Sat Jun 7 23:58:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zeo_60041/06_2025/8zeo_60041_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zeo_60041/06_2025/8zeo_60041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zeo_60041/06_2025/8zeo_60041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zeo_60041/06_2025/8zeo_60041.map" model { file = "/net/cci-nas-00/data/ceres_data/8zeo_60041/06_2025/8zeo_60041_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zeo_60041/06_2025/8zeo_60041_trim.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.095 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 12 5.49 5 S 53 5.16 5 C 5673 2.51 5 N 1553 2.21 5 O 1762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9055 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1162 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "C" Number of atoms: 2924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2924 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 359} Chain breaks: 1 Chain: "D" Number of atoms: 3729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3729 Classifications: {'peptide': 476} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 457} Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1166 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 145} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' ZN': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' ZN': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2200 SG CYS C 244 54.586 45.993 51.360 1.00 72.46 S ATOM 2661 SG CYS C 305 57.356 45.094 49.527 1.00 59.03 S ATOM 5867 SG CYS D 244 67.274 45.175 81.288 1.00 71.96 S ATOM 6328 SG CYS D 305 66.929 45.429 84.684 1.00 65.77 S Time building chain proxies: 6.27, per 1000 atoms: 0.69 Number of scatterers: 9055 At special positions: 0 Unit cell: (103.576, 102.72, 131.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 53 16.00 P 12 15.00 O 1762 8.00 N 1553 7.00 C 5673 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 305 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 191 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 244 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" SG CYS D 305 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 191 " pdb="ZN ZN D 502 " - pdb=" SG CYS D 244 " 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 11 sheets defined 49.1% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'B' and resid 67 through 84 removed outlier: 3.813A pdb=" N ILE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.699A pdb=" N PHE B 136 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'B' and resid 177 through 190 Processing helix chain 'B' and resid 192 through 211 Processing helix chain 'C' and resid 122 through 142 Processing helix chain 'C' and resid 143 through 146 Processing helix chain 'C' and resid 147 through 150 removed outlier: 4.140A pdb=" N LYS C 150 " --> pdb=" O GLY C 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 150' Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.716A pdb=" N ILE C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 214 Processing helix chain 'C' and resid 215 through 218 Processing helix chain 'C' and resid 258 through 264 removed outlier: 3.946A pdb=" N GLN C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 297 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 318 through 323 removed outlier: 4.056A pdb=" N LEU C 322 " --> pdb=" O GLN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 350 Processing helix chain 'C' and resid 351 through 354 Processing helix chain 'C' and resid 428 through 443 Processing helix chain 'C' and resid 452 through 460 removed outlier: 4.078A pdb=" N SER C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 477 Processing helix chain 'C' and resid 486 through 490 Processing helix chain 'D' and resid 23 through 34 removed outlier: 3.938A pdb=" N LYS D 27 " --> pdb=" O PRO D 23 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY D 34 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 49 Processing helix chain 'D' and resid 87 through 105 removed outlier: 3.752A pdb=" N ALA D 91 " --> pdb=" O LYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 142 removed outlier: 3.791A pdb=" N ASN D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 146 Processing helix chain 'D' and resid 147 through 150 removed outlier: 3.919A pdb=" N LYS D 150 " --> pdb=" O GLY D 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 147 through 150' Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.824A pdb=" N ILE D 180 " --> pdb=" O GLY D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 214 Processing helix chain 'D' and resid 215 through 218 Processing helix chain 'D' and resid 245 through 250 Processing helix chain 'D' and resid 258 through 264 removed outlier: 4.188A pdb=" N GLN D 262 " --> pdb=" O SER D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 318 through 323 removed outlier: 4.048A pdb=" N LEU D 322 " --> pdb=" O GLN D 318 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER D 323 " --> pdb=" O GLY D 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 318 through 323' Processing helix chain 'D' and resid 341 through 350 Processing helix chain 'D' and resid 351 through 354 Processing helix chain 'D' and resid 377 through 382 Processing helix chain 'D' and resid 428 through 443 Processing helix chain 'D' and resid 452 through 459 Processing helix chain 'D' and resid 460 through 477 Processing helix chain 'D' and resid 486 through 491 removed outlier: 3.820A pdb=" N MET D 491 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 84 removed outlier: 3.657A pdb=" N GLN E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'E' and resid 104 through 109 removed outlier: 4.766A pdb=" N GLN E 109 " --> pdb=" O THR E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 123 through 131 removed outlier: 3.528A pdb=" N GLN E 131 " --> pdb=" O MET E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 160 through 170 removed outlier: 3.627A pdb=" N VAL E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 191 removed outlier: 3.579A pdb=" N ARG E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 211 removed outlier: 3.748A pdb=" N GLN E 201 " --> pdb=" O GLN E 197 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA E 202 " --> pdb=" O LYS E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 216 Processing sheet with id=AA1, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.547A pdb=" N VAL C 155 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU C 168 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA C 153 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER C 332 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N PHE C 235 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE C 334 " --> pdb=" O PHE C 235 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C 237 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL C 336 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE C 239 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER C 332 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLY C 370 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE C 334 " --> pdb=" O GLY C 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 87 through 89 removed outlier: 3.734A pdb=" N MET C 392 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 220 through 222 Processing sheet with id=AA4, first strand: chain 'C' and resid 277 through 279 Processing sheet with id=AA5, first strand: chain 'C' and resid 411 through 412 Processing sheet with id=AA6, first strand: chain 'D' and resid 74 through 75 removed outlier: 3.843A pdb=" N LEU D 75 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 368 through 371 removed outlier: 6.788A pdb=" N SER D 332 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLY D 370 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE D 334 " --> pdb=" O GLY D 370 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE D 235 " --> pdb=" O SER D 333 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ALA D 335 " --> pdb=" O PHE D 235 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU D 237 " --> pdb=" O ALA D 335 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA D 153 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU D 168 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL D 155 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N MET D 392 " --> pdb=" O THR D 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 368 through 371 removed outlier: 6.788A pdb=" N SER D 332 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLY D 370 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE D 334 " --> pdb=" O GLY D 370 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE D 235 " --> pdb=" O SER D 333 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ALA D 335 " --> pdb=" O PHE D 235 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU D 237 " --> pdb=" O ALA D 335 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA D 153 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU D 168 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL D 155 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 220 through 222 Processing sheet with id=AB1, first strand: chain 'D' and resid 277 through 279 Processing sheet with id=AB2, first strand: chain 'D' and resid 411 through 414 405 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1542 1.31 - 1.44: 2219 1.44 - 1.57: 5341 1.57 - 1.69: 11 1.69 - 1.82: 84 Bond restraints: 9197 Sorted by residual: bond pdb=" CA VAL E 149 " pdb=" C VAL E 149 " ideal model delta sigma weight residual 1.522 1.406 0.116 1.08e-02 8.57e+03 1.16e+02 bond pdb=" CA GLU E 150 " pdb=" C GLU E 150 " ideal model delta sigma weight residual 1.523 1.412 0.111 1.34e-02 5.57e+03 6.90e+01 bond pdb=" N GLN E 157 " pdb=" CA GLN E 157 " ideal model delta sigma weight residual 1.457 1.373 0.084 1.29e-02 6.01e+03 4.23e+01 bond pdb=" CA ARG E 156 " pdb=" C ARG E 156 " ideal model delta sigma weight residual 1.523 1.444 0.079 1.34e-02 5.57e+03 3.47e+01 bond pdb=" N GLU E 150 " pdb=" CA GLU E 150 " ideal model delta sigma weight residual 1.457 1.387 0.071 1.29e-02 6.01e+03 3.00e+01 ... (remaining 9192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.85: 12397 5.85 - 11.70: 30 11.70 - 17.55: 5 17.55 - 23.39: 1 23.39 - 29.24: 1 Bond angle restraints: 12434 Sorted by residual: angle pdb=" N THR E 151 " pdb=" CA THR E 151 " pdb=" C THR E 151 " ideal model delta sigma weight residual 113.97 93.46 20.51 1.28e+00 6.10e-01 2.57e+02 angle pdb=" N LYS E 146 " pdb=" CA LYS E 146 " pdb=" C LYS E 146 " ideal model delta sigma weight residual 108.79 123.22 -14.43 1.53e+00 4.27e-01 8.90e+01 angle pdb=" N GLN E 157 " pdb=" CA GLN E 157 " pdb=" C GLN E 157 " ideal model delta sigma weight residual 110.80 94.62 16.18 2.13e+00 2.20e-01 5.77e+01 angle pdb=" C LEU E 154 " pdb=" N PRO E 155 " pdb=" CD PRO E 155 " ideal model delta sigma weight residual 125.00 95.76 29.24 4.10e+00 5.95e-02 5.09e+01 angle pdb=" N GLN E 152 " pdb=" CA GLN E 152 " pdb=" C GLN E 152 " ideal model delta sigma weight residual 110.80 95.71 15.09 2.13e+00 2.20e-01 5.02e+01 ... (remaining 12429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.95: 5320 27.95 - 55.91: 315 55.91 - 83.86: 48 83.86 - 111.82: 14 111.82 - 139.77: 8 Dihedral angle restraints: 5705 sinusoidal: 2361 harmonic: 3344 Sorted by residual: dihedral pdb=" C ARG E 156 " pdb=" N ARG E 156 " pdb=" CA ARG E 156 " pdb=" CB ARG E 156 " ideal model delta harmonic sigma weight residual -122.60 -109.71 -12.89 0 2.50e+00 1.60e-01 2.66e+01 dihedral pdb=" C6 IHP D 501 " pdb=" C1 IHP D 501 " pdb=" C2 IHP D 501 " pdb=" O12 IHP D 501 " ideal model delta sinusoidal sigma weight residual 61.05 -159.18 -139.77 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" N GLN E 157 " pdb=" C GLN E 157 " pdb=" CA GLN E 157 " pdb=" CB GLN E 157 " ideal model delta harmonic sigma weight residual 122.80 112.30 10.50 0 2.50e+00 1.60e-01 1.76e+01 ... (remaining 5702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.967: 1418 0.967 - 1.935: 0 1.935 - 2.902: 0 2.902 - 3.870: 0 3.870 - 4.837: 8 Chirality restraints: 1426 Sorted by residual: chirality pdb=" C2 IHP D 501 " pdb=" C1 IHP D 501 " pdb=" C3 IHP D 501 " pdb=" O12 IHP D 501 " both_signs ideal model delta sigma weight residual False -2.52 2.32 -4.84 2.00e-01 2.50e+01 5.85e+02 chirality pdb=" C2 IHP C 501 " pdb=" C1 IHP C 501 " pdb=" C3 IHP C 501 " pdb=" O12 IHP C 501 " both_signs ideal model delta sigma weight residual False -2.52 2.30 -4.82 2.00e-01 2.50e+01 5.81e+02 chirality pdb=" C5 IHP C 501 " pdb=" C4 IHP C 501 " pdb=" C6 IHP C 501 " pdb=" O15 IHP C 501 " both_signs ideal model delta sigma weight residual False -2.42 2.28 -4.70 2.00e-01 2.50e+01 5.52e+02 ... (remaining 1423 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 154 " -0.137 5.00e-02 4.00e+02 2.07e-01 6.89e+01 pdb=" N PRO E 155 " 0.358 5.00e-02 4.00e+02 pdb=" CA PRO E 155 " -0.133 5.00e-02 4.00e+02 pdb=" CD PRO E 155 " -0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 144 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C ILE E 144 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE E 144 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS E 145 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 154 " 0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO B 155 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 155 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 155 " 0.028 5.00e-02 4.00e+02 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 196 2.67 - 3.23: 9020 3.23 - 3.78: 14481 3.78 - 4.34: 19852 4.34 - 4.90: 31979 Nonbonded interactions: 75528 Sorted by model distance: nonbonded pdb=" O GLN E 157 " pdb=" N ASP E 159 " model vdw 2.108 3.120 nonbonded pdb=" O THR E 151 " pdb=" C GLN E 152 " model vdw 2.131 3.270 nonbonded pdb=" N THR E 151 " pdb=" N GLN E 152 " model vdw 2.189 2.560 nonbonded pdb=" OE1 GLU D 368 " pdb=" OG SER E 106 " model vdw 2.227 3.040 nonbonded pdb=" O GLN E 157 " pdb=" C MET E 158 " model vdw 2.272 3.270 ... (remaining 75523 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 'B' and (resid 67 through 98 or (resid 99 and (name N or name CA or name \ C or name O or name CB )) or resid 100 through 148 or (resid 149 and (name N or \ name CA or name C or name O or name CB )) or resid 150 through 217)) selection = (chain 'E' and resid 67 through 217) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.330 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.015 0.748 9205 Z= 1.097 Angle : 0.907 29.243 12434 Z= 0.471 Chirality : 0.355 4.837 1426 Planarity : 0.007 0.207 1590 Dihedral : 18.712 139.774 3533 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.47 % Favored : 94.92 % Rotamer: Outliers : 2.12 % Allowed : 21.54 % Favored : 76.34 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1142 helix: 1.04 (0.24), residues: 462 sheet: 0.59 (0.52), residues: 125 loop : 0.07 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 482 HIS 0.003 0.001 HIS C 236 PHE 0.022 0.002 PHE E 177 TYR 0.012 0.001 TYR C 330 ARG 0.008 0.001 ARG D 344 Details of bonding type rmsd hydrogen bonds : bond 0.17916 ( 392) hydrogen bonds : angle 6.03503 ( 1119) metal coordination : bond 0.32083 ( 6) covalent geometry : bond 0.00775 ( 9197) covalent geometry : angle 0.90679 (12434) Misc. bond : bond 0.65857 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: B 82 GLN cc_start: 0.6901 (mt0) cc_final: 0.6355 (mp10) REVERT: B 127 MET cc_start: 0.7076 (mtp) cc_final: 0.6653 (mpp) REVERT: B 176 GLN cc_start: 0.6770 (tp-100) cc_final: 0.6456 (tt0) REVERT: B 209 LYS cc_start: 0.7499 (tppp) cc_final: 0.7154 (tttm) REVERT: C 176 ARG cc_start: 0.7446 (mtp85) cc_final: 0.7191 (mtp85) REVERT: C 214 GLU cc_start: 0.6290 (mt-10) cc_final: 0.5847 (pt0) REVERT: C 222 LYS cc_start: 0.8274 (tptt) cc_final: 0.8018 (tppt) REVERT: C 266 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7159 (mtt-85) REVERT: C 299 ARG cc_start: 0.7727 (mtm180) cc_final: 0.7427 (mtp180) REVERT: C 338 GLU cc_start: 0.7145 (pp20) cc_final: 0.6908 (mt-10) REVERT: C 341 ASN cc_start: 0.7137 (m-40) cc_final: 0.6812 (p0) REVERT: C 343 ASP cc_start: 0.7411 (p0) cc_final: 0.7192 (p0) REVERT: C 344 ARG cc_start: 0.7072 (ttm-80) cc_final: 0.6381 (ttm-80) REVERT: C 347 LYS cc_start: 0.7201 (ttmm) cc_final: 0.6460 (tmtm) REVERT: C 357 LYS cc_start: 0.8480 (tppt) cc_final: 0.8261 (mmtt) REVERT: C 416 MET cc_start: 0.4410 (pmm) cc_final: 0.4134 (pmt) REVERT: C 430 LYS cc_start: 0.7243 (tmtm) cc_final: 0.6600 (tmmt) REVERT: D 140 LYS cc_start: 0.7554 (ttmm) cc_final: 0.7071 (mptt) REVERT: D 176 ARG cc_start: 0.8116 (mtm-85) cc_final: 0.7829 (mtm180) REVERT: D 437 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7293 (mp) REVERT: D 462 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7804 (mt-10) REVERT: E 72 LYS cc_start: 0.7038 (ttmt) cc_final: 0.6338 (tppt) REVERT: E 127 MET cc_start: 0.7890 (mtm) cc_final: 0.7682 (mtt) REVERT: E 132 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6139 (m-30) REVERT: E 137 LYS cc_start: 0.8187 (mmmm) cc_final: 0.7848 (mptt) REVERT: E 201 GLN cc_start: 0.6140 (mp10) cc_final: 0.5867 (mp10) outliers start: 21 outliers final: 6 residues processed: 159 average time/residue: 1.4522 time to fit residues: 244.6362 Evaluate side-chains 124 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain E residue 132 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 0.0170 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 ASN D 263 ASN ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN E 170 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.193984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.142639 restraints weight = 9272.124| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.15 r_work: 0.3317 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 9205 Z= 0.142 Angle : 0.729 21.978 12434 Z= 0.334 Chirality : 0.050 0.580 1426 Planarity : 0.006 0.184 1590 Dihedral : 10.160 100.724 1325 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.64 % Favored : 95.18 % Rotamer: Outliers : 4.25 % Allowed : 18.20 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), residues: 1142 helix: 1.14 (0.24), residues: 456 sheet: 1.68 (0.56), residues: 89 loop : 0.05 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 473 HIS 0.003 0.001 HIS C 130 PHE 0.013 0.001 PHE C 124 TYR 0.013 0.001 TYR D 453 ARG 0.006 0.001 ARG D 344 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 392) hydrogen bonds : angle 4.62408 ( 1119) metal coordination : bond 0.00366 ( 6) covalent geometry : bond 0.00336 ( 9197) covalent geometry : angle 0.72945 (12434) Misc. bond : bond 0.00057 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 1.229 Fit side-chains REVERT: B 81 ILE cc_start: 0.6653 (OUTLIER) cc_final: 0.6437 (pp) REVERT: B 82 GLN cc_start: 0.7358 (mt0) cc_final: 0.6918 (mp10) REVERT: B 127 MET cc_start: 0.7356 (mtp) cc_final: 0.7112 (mpp) REVERT: B 175 ASP cc_start: 0.6413 (t0) cc_final: 0.5960 (t70) REVERT: B 209 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7233 (tttm) REVERT: C 140 LYS cc_start: 0.7586 (tptt) cc_final: 0.7217 (mppt) REVERT: C 266 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.7735 (mmm160) REVERT: C 296 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6779 (mmm) REVERT: C 299 ARG cc_start: 0.8158 (mtm180) cc_final: 0.7926 (mtp180) REVERT: C 344 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7196 (ttm-80) REVERT: C 347 LYS cc_start: 0.8123 (ttmm) cc_final: 0.7659 (tmtm) REVERT: C 430 LYS cc_start: 0.8250 (tmtm) cc_final: 0.7865 (tmmt) REVERT: C 462 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8293 (mp0) REVERT: D 122 THR cc_start: 0.7615 (p) cc_final: 0.7411 (p) REVERT: D 140 LYS cc_start: 0.7596 (ttmm) cc_final: 0.7172 (mptt) REVERT: D 286 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6997 (tt0) REVERT: D 437 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8035 (mp) REVERT: E 131 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7287 (mp10) REVERT: E 201 GLN cc_start: 0.6219 (mp10) cc_final: 0.5982 (mp-120) outliers start: 42 outliers final: 11 residues processed: 142 average time/residue: 1.5813 time to fit residues: 239.8309 Evaluate side-chains 123 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain E residue 141 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 44 optimal weight: 0.0370 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 170 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.194404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149282 restraints weight = 9374.582| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.78 r_work: 0.3326 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 9205 Z= 0.125 Angle : 0.611 18.241 12434 Z= 0.292 Chirality : 0.048 0.482 1426 Planarity : 0.006 0.170 1590 Dihedral : 9.908 94.510 1320 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.47 % Favored : 95.36 % Rotamer: Outliers : 3.54 % Allowed : 18.71 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1142 helix: 1.02 (0.24), residues: 477 sheet: 1.58 (0.56), residues: 89 loop : -0.06 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.003 0.001 HIS D 130 PHE 0.013 0.001 PHE C 124 TYR 0.012 0.001 TYR D 453 ARG 0.003 0.000 ARG D 344 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 392) hydrogen bonds : angle 4.32153 ( 1119) metal coordination : bond 0.00186 ( 6) covalent geometry : bond 0.00300 ( 9197) covalent geometry : angle 0.61130 (12434) Misc. bond : bond 0.00020 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 1.200 Fit side-chains REVERT: B 82 GLN cc_start: 0.7354 (mt0) cc_final: 0.6958 (mp10) REVERT: B 175 ASP cc_start: 0.6371 (t0) cc_final: 0.5944 (t70) REVERT: C 140 LYS cc_start: 0.7599 (tptt) cc_final: 0.7320 (tppt) REVERT: C 266 ARG cc_start: 0.8611 (mtm-85) cc_final: 0.7801 (mmm160) REVERT: C 296 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6798 (mmm) REVERT: C 344 ARG cc_start: 0.7859 (ttm-80) cc_final: 0.7252 (ttm-80) REVERT: C 347 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7706 (tmtm) REVERT: C 430 LYS cc_start: 0.8325 (tmtm) cc_final: 0.7963 (tmmt) REVERT: C 494 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8291 (mt) REVERT: D 140 LYS cc_start: 0.7605 (ttmm) cc_final: 0.7096 (mptt) REVERT: E 198 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6920 (ptmm) outliers start: 35 outliers final: 10 residues processed: 142 average time/residue: 1.6650 time to fit residues: 250.9427 Evaluate side-chains 121 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 198 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 chunk 16 optimal weight: 0.0970 chunk 89 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.205838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.154142 restraints weight = 9407.580| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.74 r_work: 0.3504 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 9205 Z= 0.119 Angle : 0.588 16.208 12434 Z= 0.285 Chirality : 0.047 0.483 1426 Planarity : 0.006 0.162 1590 Dihedral : 9.758 95.064 1318 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.47 % Favored : 95.36 % Rotamer: Outliers : 3.44 % Allowed : 19.51 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1142 helix: 1.10 (0.24), residues: 471 sheet: 0.90 (0.54), residues: 99 loop : -0.10 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 473 HIS 0.002 0.001 HIS D 130 PHE 0.013 0.001 PHE C 124 TYR 0.009 0.001 TYR D 453 ARG 0.003 0.000 ARG D 311 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 392) hydrogen bonds : angle 4.25195 ( 1119) metal coordination : bond 0.00154 ( 6) covalent geometry : bond 0.00286 ( 9197) covalent geometry : angle 0.58802 (12434) Misc. bond : bond 0.00039 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.130 Fit side-chains REVERT: B 82 GLN cc_start: 0.7358 (mt0) cc_final: 0.6912 (mp10) REVERT: B 143 ASN cc_start: 0.8016 (m-40) cc_final: 0.7762 (m110) REVERT: B 175 ASP cc_start: 0.6370 (t0) cc_final: 0.6024 (t70) REVERT: C 137 GLU cc_start: 0.7917 (tp30) cc_final: 0.7551 (mt-10) REVERT: C 140 LYS cc_start: 0.7527 (tptt) cc_final: 0.7245 (tppt) REVERT: C 146 TYR cc_start: 0.7659 (t80) cc_final: 0.7169 (m-80) REVERT: C 222 LYS cc_start: 0.8460 (tptt) cc_final: 0.8160 (tppt) REVERT: C 266 ARG cc_start: 0.8590 (mtm-85) cc_final: 0.7764 (mmm160) REVERT: C 296 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6745 (mmm) REVERT: C 344 ARG cc_start: 0.7701 (ttm-80) cc_final: 0.7189 (ttm-80) REVERT: C 347 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7599 (tmtm) REVERT: C 430 LYS cc_start: 0.8295 (tmtm) cc_final: 0.7891 (tmmt) REVERT: C 494 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8187 (mt) REVERT: D 140 LYS cc_start: 0.7580 (ttmm) cc_final: 0.7045 (mptt) REVERT: D 286 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.7071 (tt0) REVERT: E 198 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7186 (ptmm) outliers start: 34 outliers final: 16 residues processed: 139 average time/residue: 1.2820 time to fit residues: 189.9784 Evaluate side-chains 127 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 198 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 88 optimal weight: 0.0970 chunk 74 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 10 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 0.0000 chunk 7 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 ASN C 263 ASN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.206927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.155148 restraints weight = 9466.404| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.63 r_work: 0.3498 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 9205 Z= 0.108 Angle : 0.566 14.858 12434 Z= 0.276 Chirality : 0.046 0.433 1426 Planarity : 0.005 0.157 1590 Dihedral : 9.492 91.836 1318 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.29 % Favored : 95.53 % Rotamer: Outliers : 3.44 % Allowed : 19.51 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1142 helix: 1.12 (0.24), residues: 478 sheet: 0.90 (0.53), residues: 99 loop : -0.10 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 473 HIS 0.003 0.001 HIS D 130 PHE 0.012 0.001 PHE C 124 TYR 0.008 0.001 TYR D 453 ARG 0.004 0.000 ARG D 344 Details of bonding type rmsd hydrogen bonds : bond 0.03084 ( 392) hydrogen bonds : angle 4.16652 ( 1119) metal coordination : bond 0.00112 ( 6) covalent geometry : bond 0.00258 ( 9197) covalent geometry : angle 0.56586 (12434) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 1.004 Fit side-chains REVERT: B 82 GLN cc_start: 0.7331 (mt0) cc_final: 0.6896 (mp10) REVERT: B 143 ASN cc_start: 0.8082 (m-40) cc_final: 0.7796 (m110) REVERT: B 209 LYS cc_start: 0.7313 (tttm) cc_final: 0.6814 (ptmm) REVERT: C 137 GLU cc_start: 0.8042 (tp30) cc_final: 0.7652 (mt-10) REVERT: C 140 LYS cc_start: 0.7570 (tptt) cc_final: 0.7215 (mttp) REVERT: C 146 TYR cc_start: 0.7648 (t80) cc_final: 0.7135 (m-80) REVERT: C 222 LYS cc_start: 0.8479 (tptt) cc_final: 0.8199 (tppt) REVERT: C 266 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.7763 (mmm160) REVERT: C 296 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6772 (mmm) REVERT: C 344 ARG cc_start: 0.7749 (ttm-80) cc_final: 0.7216 (ttm-80) REVERT: C 347 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7630 (tmtm) REVERT: C 430 LYS cc_start: 0.8311 (tmtm) cc_final: 0.7920 (tmmt) REVERT: D 140 LYS cc_start: 0.7585 (ttmm) cc_final: 0.7037 (mptt) outliers start: 34 outliers final: 15 residues processed: 131 average time/residue: 1.4554 time to fit residues: 203.4770 Evaluate side-chains 121 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 141 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 65 optimal weight: 0.2980 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 39 optimal weight: 0.0970 chunk 29 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 152 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.196453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.154589 restraints weight = 9312.812| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.69 r_work: 0.3414 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 9205 Z= 0.105 Angle : 0.556 13.985 12434 Z= 0.271 Chirality : 0.045 0.408 1426 Planarity : 0.005 0.153 1590 Dihedral : 9.306 89.665 1318 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.38 % Favored : 95.45 % Rotamer: Outliers : 3.54 % Allowed : 19.62 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1142 helix: 1.15 (0.24), residues: 479 sheet: 0.90 (0.53), residues: 99 loop : -0.07 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 473 HIS 0.003 0.001 HIS D 130 PHE 0.013 0.001 PHE E 177 TYR 0.007 0.001 TYR C 205 ARG 0.004 0.000 ARG D 344 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 392) hydrogen bonds : angle 4.10035 ( 1119) metal coordination : bond 0.00126 ( 6) covalent geometry : bond 0.00251 ( 9197) covalent geometry : angle 0.55608 (12434) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.860 Fit side-chains REVERT: B 82 GLN cc_start: 0.7534 (mt0) cc_final: 0.7269 (mp10) REVERT: B 176 GLN cc_start: 0.7631 (mt0) cc_final: 0.7281 (mt0) REVERT: B 209 LYS cc_start: 0.7332 (tttm) cc_final: 0.6865 (ptmm) REVERT: C 140 LYS cc_start: 0.7564 (tptt) cc_final: 0.7300 (mtmm) REVERT: C 214 GLU cc_start: 0.7004 (pt0) cc_final: 0.6748 (pt0) REVERT: C 266 ARG cc_start: 0.8497 (mtm-85) cc_final: 0.7925 (mmm160) REVERT: C 296 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6499 (mmm) REVERT: C 344 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7272 (ttm-80) REVERT: C 430 LYS cc_start: 0.8154 (tmtm) cc_final: 0.7908 (tmmt) REVERT: D 140 LYS cc_start: 0.7547 (ttmm) cc_final: 0.7114 (mptt) REVERT: E 189 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.5923 (mtp180) REVERT: E 198 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7293 (ptmm) outliers start: 35 outliers final: 17 residues processed: 134 average time/residue: 1.5279 time to fit residues: 217.2571 Evaluate side-chains 119 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 189 ARG Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 201 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 12 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 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 143 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN E 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.205133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.157114 restraints weight = 9489.784| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.09 r_work: 0.3499 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 9205 Z= 0.133 Angle : 0.591 13.569 12434 Z= 0.289 Chirality : 0.048 0.491 1426 Planarity : 0.005 0.151 1590 Dihedral : 9.423 92.721 1317 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.55 % Favored : 95.27 % Rotamer: Outliers : 3.54 % Allowed : 20.02 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1142 helix: 1.07 (0.23), residues: 472 sheet: 0.72 (0.53), residues: 101 loop : -0.06 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 482 HIS 0.003 0.001 HIS D 130 PHE 0.014 0.001 PHE E 177 TYR 0.024 0.001 TYR C 146 ARG 0.003 0.000 ARG D 311 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 392) hydrogen bonds : angle 4.17550 ( 1119) metal coordination : bond 0.00204 ( 6) covalent geometry : bond 0.00325 ( 9197) covalent geometry : angle 0.59145 (12434) Misc. bond : bond 0.00064 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.989 Fit side-chains REVERT: B 82 GLN cc_start: 0.7346 (mt0) cc_final: 0.6971 (mp10) REVERT: B 176 GLN cc_start: 0.7635 (mt0) cc_final: 0.7281 (mt0) REVERT: B 209 LYS cc_start: 0.7345 (tttm) cc_final: 0.6842 (ptmm) REVERT: C 140 LYS cc_start: 0.7443 (tptt) cc_final: 0.7131 (mttp) REVERT: C 266 ARG cc_start: 0.8578 (mtm-85) cc_final: 0.7835 (mmm160) REVERT: C 296 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6790 (mmm) REVERT: C 344 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.7124 (ttm-80) REVERT: C 430 LYS cc_start: 0.8334 (tmtm) cc_final: 0.7982 (tmmt) REVERT: C 462 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8463 (mp0) REVERT: E 189 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.5763 (mtp180) REVERT: E 198 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7273 (ptmm) outliers start: 35 outliers final: 18 residues processed: 127 average time/residue: 1.4275 time to fit residues: 193.1582 Evaluate side-chains 126 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 189 ARG Chi-restraints excluded: chain E residue 198 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 29 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 86 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN E 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.198919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.143874 restraints weight = 9461.793| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.86 r_work: 0.3407 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 9205 Z= 0.283 Angle : 0.768 13.938 12434 Z= 0.367 Chirality : 0.063 0.862 1426 Planarity : 0.006 0.152 1590 Dihedral : 10.525 107.048 1317 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.08 % Favored : 94.75 % Rotamer: Outliers : 3.44 % Allowed : 19.41 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1142 helix: 0.54 (0.23), residues: 468 sheet: 1.32 (0.57), residues: 85 loop : -0.25 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 482 HIS 0.007 0.002 HIS C 324 PHE 0.022 0.002 PHE E 177 TYR 0.021 0.002 TYR C 146 ARG 0.005 0.001 ARG C 311 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 392) hydrogen bonds : angle 4.59118 ( 1119) metal coordination : bond 0.00599 ( 6) covalent geometry : bond 0.00698 ( 9197) covalent geometry : angle 0.76760 (12434) Misc. bond : bond 0.00235 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 1.716 Fit side-chains REVERT: B 78 LEU cc_start: 0.7052 (mt) cc_final: 0.6754 (mt) REVERT: B 82 GLN cc_start: 0.7267 (mt0) cc_final: 0.6823 (mp10) REVERT: B 176 GLN cc_start: 0.7679 (mt0) cc_final: 0.7332 (mt0) REVERT: C 140 LYS cc_start: 0.7472 (tptt) cc_final: 0.6628 (mmpt) REVERT: C 266 ARG cc_start: 0.8609 (mtm-85) cc_final: 0.7783 (mtm180) REVERT: C 296 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7095 (mmp) REVERT: C 344 ARG cc_start: 0.7715 (ttm-80) cc_final: 0.7136 (ttm-80) REVERT: C 430 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8024 (tmmt) REVERT: D 140 LYS cc_start: 0.7810 (ttmm) cc_final: 0.7282 (mptt) REVERT: D 479 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8561 (mm) REVERT: E 72 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7056 (tppt) REVERT: E 189 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.5790 (mtp180) REVERT: E 198 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7283 (ptmm) outliers start: 34 outliers final: 17 residues processed: 131 average time/residue: 1.6615 time to fit residues: 231.3908 Evaluate side-chains 128 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 430 LYS Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 189 ARG Chi-restraints excluded: chain E residue 198 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 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 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN E 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.203493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.153270 restraints weight = 9346.456| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.15 r_work: 0.3470 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 9205 Z= 0.136 Angle : 0.607 13.344 12434 Z= 0.297 Chirality : 0.049 0.518 1426 Planarity : 0.006 0.150 1590 Dihedral : 10.004 98.796 1314 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.64 % Favored : 95.18 % Rotamer: Outliers : 2.73 % Allowed : 20.12 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.25), residues: 1142 helix: 0.82 (0.24), residues: 461 sheet: 0.99 (0.55), residues: 92 loop : -0.05 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 473 HIS 0.005 0.001 HIS D 130 PHE 0.018 0.001 PHE E 177 TYR 0.021 0.001 TYR C 146 ARG 0.003 0.000 ARG C 405 Details of bonding type rmsd hydrogen bonds : bond 0.03322 ( 392) hydrogen bonds : angle 4.28318 ( 1119) metal coordination : bond 0.00164 ( 6) covalent geometry : bond 0.00329 ( 9197) covalent geometry : angle 0.60652 (12434) Misc. bond : bond 0.00085 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.990 Fit side-chains REVERT: B 82 GLN cc_start: 0.7326 (mt0) cc_final: 0.6957 (mp10) REVERT: B 176 GLN cc_start: 0.7701 (mt0) cc_final: 0.7335 (mt0) REVERT: C 140 LYS cc_start: 0.7501 (tptt) cc_final: 0.6622 (mmpt) REVERT: C 149 GLU cc_start: 0.7964 (pm20) cc_final: 0.7600 (pt0) REVERT: C 266 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.7896 (mmm160) REVERT: C 296 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.6896 (mmp) REVERT: C 344 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7327 (ttm-80) REVERT: C 416 MET cc_start: 0.4971 (OUTLIER) cc_final: 0.4279 (ptt) REVERT: C 430 LYS cc_start: 0.8461 (tmtm) cc_final: 0.8076 (tmmt) REVERT: D 140 LYS cc_start: 0.7709 (ttmm) cc_final: 0.7310 (mptt) REVERT: E 189 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.5706 (mtp180) REVERT: E 198 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7365 (ptmm) outliers start: 27 outliers final: 14 residues processed: 119 average time/residue: 1.4798 time to fit residues: 187.1150 Evaluate side-chains 119 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain E residue 189 ARG Chi-restraints excluded: chain E residue 198 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 0.1980 chunk 111 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 60 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN E 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.204028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.152269 restraints weight = 9465.133| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.28 r_work: 0.3472 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 9205 Z= 0.134 Angle : 0.602 12.906 12434 Z= 0.295 Chirality : 0.049 0.519 1426 Planarity : 0.005 0.148 1590 Dihedral : 9.763 97.129 1314 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.90 % Favored : 94.92 % Rotamer: Outliers : 2.43 % Allowed : 20.53 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1142 helix: 0.88 (0.24), residues: 461 sheet: 1.38 (0.57), residues: 85 loop : -0.04 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 473 HIS 0.005 0.001 HIS D 130 PHE 0.018 0.001 PHE E 177 TYR 0.018 0.001 TYR C 146 ARG 0.003 0.000 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 392) hydrogen bonds : angle 4.25485 ( 1119) metal coordination : bond 0.00187 ( 6) covalent geometry : bond 0.00325 ( 9197) covalent geometry : angle 0.60157 (12434) Misc. bond : bond 0.00069 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 1.043 Fit side-chains REVERT: B 82 GLN cc_start: 0.7229 (mt0) cc_final: 0.6884 (mp10) REVERT: B 176 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7336 (mt0) REVERT: B 209 LYS cc_start: 0.7370 (tttm) cc_final: 0.6901 (ptmm) REVERT: C 140 LYS cc_start: 0.7545 (tptt) cc_final: 0.6824 (mmpt) REVERT: C 149 GLU cc_start: 0.7836 (pm20) cc_final: 0.7493 (pt0) REVERT: C 266 ARG cc_start: 0.8480 (mtm-85) cc_final: 0.7757 (mmm160) REVERT: C 296 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6715 (mmm) REVERT: C 416 MET cc_start: 0.5009 (OUTLIER) cc_final: 0.4182 (ptt) REVERT: C 430 LYS cc_start: 0.8277 (tmtm) cc_final: 0.7888 (tmmt) REVERT: D 140 LYS cc_start: 0.7619 (ttmm) cc_final: 0.7272 (mptt) REVERT: E 189 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.5816 (mtp180) REVERT: E 198 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7250 (ptmm) outliers start: 24 outliers final: 16 residues processed: 112 average time/residue: 1.4837 time to fit residues: 176.5319 Evaluate side-chains 119 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 189 ARG Chi-restraints excluded: chain E residue 198 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 110 optimal weight: 0.6980 chunk 35 optimal weight: 0.0970 chunk 106 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN E 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.206112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.156301 restraints weight = 9470.176| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.26 r_work: 0.3494 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 9205 Z= 0.116 Angle : 0.571 12.484 12434 Z= 0.282 Chirality : 0.046 0.433 1426 Planarity : 0.005 0.146 1590 Dihedral : 9.524 93.253 1314 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.29 % Favored : 95.53 % Rotamer: Outliers : 2.33 % Allowed : 20.93 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1142 helix: 0.95 (0.24), residues: 467 sheet: 1.07 (0.56), residues: 92 loop : 0.02 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 473 HIS 0.005 0.001 HIS D 130 PHE 0.015 0.001 PHE E 177 TYR 0.017 0.001 TYR C 146 ARG 0.004 0.000 ARG B 87 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 392) hydrogen bonds : angle 4.18489 ( 1119) metal coordination : bond 0.00137 ( 6) covalent geometry : bond 0.00276 ( 9197) covalent geometry : angle 0.57082 (12434) Misc. bond : bond 0.00039 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8255.70 seconds wall clock time: 146 minutes 29.41 seconds (8789.41 seconds total)