Starting phenix.real_space_refine on Wed Sep 17 14:23:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zeo_60041/09_2025/8zeo_60041_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zeo_60041/09_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_60041/09_2025/8zeo_60041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zeo_60041/09_2025/8zeo_60041.map" model { file = "/net/cci-nas-00/data/ceres_data/8zeo_60041/09_2025/8zeo_60041_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zeo_60041/09_2025/8zeo_60041_trim.cif" } resolution = 2.79 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= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.30, per 1000 atoms: 0.25 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: 1.03 Conformation dependent library (CDL) restraints added in 356.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.38 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: 1.47 Time building geometry restraints manager: 1.24 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: 2.360 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.480 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.830 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG D 344 TYR 0.012 0.001 TYR C 330 PHE 0.022 0.002 PHE E 177 TRP 0.008 0.001 TRP D 482 HIS 0.003 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00775 ( 9197) covalent geometry : angle 0.90679 (12434) hydrogen bonds : bond 0.17916 ( 392) hydrogen bonds : angle 6.03503 ( 1119) metal coordination : bond 0.32083 ( 6) 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 : 0.289 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: 0.7000 time to fit residues: 117.6187 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 : 0.295 ------------------------------------------------------------------------------- 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 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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** D 263 ASN E 152 GLN E 170 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.194009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143720 restraints weight = 9309.304| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.23 r_work: 0.3296 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 9205 Z= 0.143 Angle : 0.730 21.818 12434 Z= 0.334 Chirality : 0.049 0.551 1426 Planarity : 0.006 0.184 1590 Dihedral : 10.129 100.854 1325 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.64 % Favored : 95.18 % Rotamer: Outliers : 4.25 % Allowed : 18.40 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. 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 ARG 0.006 0.001 ARG D 344 TYR 0.013 0.001 TYR D 453 PHE 0.013 0.001 PHE E 177 TRP 0.007 0.001 TRP D 473 HIS 0.003 0.001 HIS D 191 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9197) covalent geometry : angle 0.73024 (12434) hydrogen bonds : bond 0.03926 ( 392) hydrogen bonds : angle 4.60862 ( 1119) metal coordination : bond 0.00296 ( 6) Misc. bond : bond 0.00029 ( 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 : 0.354 Fit side-chains REVERT: B 81 ILE cc_start: 0.6631 (OUTLIER) cc_final: 0.6407 (pp) REVERT: B 82 GLN cc_start: 0.7355 (mt0) cc_final: 0.6895 (mp10) REVERT: B 127 MET cc_start: 0.7352 (mtp) cc_final: 0.7099 (mpp) REVERT: B 175 ASP cc_start: 0.6457 (t0) cc_final: 0.5989 (t70) REVERT: B 209 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7245 (tttm) REVERT: C 140 LYS cc_start: 0.7591 (tptt) cc_final: 0.7216 (mppt) REVERT: C 266 ARG cc_start: 0.8559 (mtm-85) cc_final: 0.7723 (mmm160) REVERT: C 296 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6828 (mmm) REVERT: C 299 ARG cc_start: 0.8173 (mtm180) cc_final: 0.7941 (mtp180) REVERT: C 344 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7226 (ttm-80) REVERT: C 347 LYS cc_start: 0.8151 (ttmm) cc_final: 0.7685 (tmtm) REVERT: C 430 LYS cc_start: 0.8290 (tmtm) cc_final: 0.7907 (tmmt) REVERT: D 140 LYS cc_start: 0.7617 (ttmm) cc_final: 0.7175 (mptt) REVERT: D 286 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7033 (tt0) REVERT: D 437 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8062 (mp) REVERT: E 131 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: E 201 GLN cc_start: 0.6236 (mp10) cc_final: 0.5994 (mp-120) outliers start: 42 outliers final: 11 residues processed: 142 average time/residue: 0.6363 time to fit residues: 96.0841 Evaluate side-chains 121 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 4 optimal weight: 0.0670 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 240 ASN C 263 ASN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.194183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.149213 restraints weight = 9225.954| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.77 r_work: 0.3269 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1706 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= 0.127 Angle : 0.614 18.352 12434 Z= 0.293 Chirality : 0.048 0.483 1426 Planarity : 0.006 0.171 1590 Dihedral : 9.919 94.839 1320 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.94 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.25), residues: 1142 helix: 1.04 (0.24), residues: 471 sheet: 1.54 (0.56), residues: 89 loop : -0.10 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 344 TYR 0.012 0.001 TYR D 453 PHE 0.012 0.001 PHE E 177 TRP 0.009 0.001 TRP D 482 HIS 0.003 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9197) covalent geometry : angle 0.61356 (12434) hydrogen bonds : bond 0.03493 ( 392) hydrogen bonds : angle 4.32529 ( 1119) metal coordination : bond 0.00182 ( 6) Misc. bond : bond 0.00076 ( 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 : 0.368 Fit side-chains REVERT: B 82 GLN cc_start: 0.7307 (mt0) cc_final: 0.6891 (mp10) REVERT: B 127 MET cc_start: 0.7261 (mtp) cc_final: 0.6994 (mpp) REVERT: B 175 ASP cc_start: 0.6306 (t0) cc_final: 0.5916 (t70) REVERT: C 140 LYS cc_start: 0.7555 (tptt) cc_final: 0.7260 (tppt) REVERT: C 266 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.7716 (mmm160) REVERT: C 296 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6725 (mmm) REVERT: C 344 ARG cc_start: 0.7761 (ttm-80) cc_final: 0.7110 (ttm-80) REVERT: C 347 LYS cc_start: 0.8011 (ttmm) cc_final: 0.7523 (tmtm) REVERT: C 430 LYS cc_start: 0.8259 (tmtm) cc_final: 0.7843 (tmmt) REVERT: C 494 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8224 (mt) REVERT: D 140 LYS cc_start: 0.7562 (ttmm) cc_final: 0.7018 (mptt) REVERT: D 286 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: E 131 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: E 198 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6838 (ptmm) REVERT: E 201 GLN cc_start: 0.6284 (mt0) cc_final: 0.6057 (mp10) outliers start: 35 outliers final: 10 residues processed: 142 average time/residue: 0.6838 time to fit residues: 104.6646 Evaluate side-chains 124 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 286 GLU 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 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 45 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 57 optimal weight: 7.9990 chunk 109 optimal weight: 0.0970 chunk 29 optimal weight: 0.2980 chunk 46 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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** ** 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 = 0.4151 r_free = 0.4151 target = 0.195820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147872 restraints weight = 9383.945| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.95 r_work: 0.3319 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 9205 Z= 0.110 Angle : 0.572 16.159 12434 Z= 0.277 Chirality : 0.046 0.450 1426 Planarity : 0.006 0.162 1590 Dihedral : 9.683 93.806 1318 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.38 % Favored : 95.45 % Rotamer: Outliers : 3.54 % Allowed : 19.51 % Favored : 76.95 % 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 aren not related in a simple way. whole: 0.73 (0.25), residues: 1142 helix: 1.17 (0.24), residues: 471 sheet: 0.91 (0.54), residues: 99 loop : -0.09 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 344 TYR 0.009 0.001 TYR D 453 PHE 0.013 0.001 PHE C 124 TRP 0.007 0.001 TRP D 473 HIS 0.002 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9197) covalent geometry : angle 0.57182 (12434) hydrogen bonds : bond 0.03148 ( 392) hydrogen bonds : angle 4.20095 ( 1119) metal coordination : bond 0.00120 ( 6) Misc. bond : bond 0.00030 ( 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 155 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.320 Fit side-chains REVERT: B 82 GLN cc_start: 0.7350 (mt0) cc_final: 0.6896 (mp10) REVERT: B 127 MET cc_start: 0.7262 (mtp) cc_final: 0.7032 (mpp) REVERT: B 175 ASP cc_start: 0.6383 (t0) cc_final: 0.6050 (t70) REVERT: C 137 GLU cc_start: 0.7936 (tp30) cc_final: 0.7596 (mt-10) REVERT: C 140 LYS cc_start: 0.7520 (tptt) cc_final: 0.7233 (tppt) REVERT: C 146 TYR cc_start: 0.7573 (t80) cc_final: 0.7137 (m-80) REVERT: C 266 ARG cc_start: 0.8590 (mtm-85) cc_final: 0.7772 (mmm160) REVERT: C 296 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6716 (mmm) REVERT: C 344 ARG cc_start: 0.7713 (ttm-80) cc_final: 0.7205 (ttm-80) REVERT: C 347 LYS cc_start: 0.8087 (ttmm) cc_final: 0.7636 (tmtm) REVERT: C 430 LYS cc_start: 0.8232 (tmtm) cc_final: 0.7846 (tmmt) REVERT: C 494 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8223 (mt) REVERT: D 140 LYS cc_start: 0.7560 (ttmm) cc_final: 0.7010 (mptt) REVERT: E 201 GLN cc_start: 0.6209 (mt0) cc_final: 0.6005 (mp10) outliers start: 35 outliers final: 16 residues processed: 143 average time/residue: 0.6365 time to fit residues: 96.8989 Evaluate side-chains 127 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 86 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 142 ASN C 263 ASN C 324 HIS ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN E 170 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.204090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.153718 restraints weight = 9443.788| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.10 r_work: 0.3490 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2087 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= 0.138 Angle : 0.604 15.080 12434 Z= 0.291 Chirality : 0.050 0.548 1426 Planarity : 0.006 0.158 1590 Dihedral : 9.736 95.741 1318 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.29 % Favored : 95.53 % Rotamer: Outliers : 3.94 % Allowed : 19.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.25), residues: 1142 helix: 1.14 (0.24), residues: 473 sheet: 1.26 (0.54), residues: 91 loop : -0.08 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 344 TYR 0.008 0.001 TYR C 205 PHE 0.013 0.001 PHE E 177 TRP 0.006 0.001 TRP D 482 HIS 0.003 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9197) covalent geometry : angle 0.60394 (12434) hydrogen bonds : bond 0.03315 ( 392) hydrogen bonds : angle 4.23373 ( 1119) metal coordination : bond 0.00256 ( 6) Misc. bond : bond 0.00076 ( 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 152 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: B 82 GLN cc_start: 0.7409 (mt0) cc_final: 0.7060 (mp10) REVERT: C 140 LYS cc_start: 0.7592 (tptt) cc_final: 0.7224 (mtmm) REVERT: C 146 TYR cc_start: 0.7544 (t80) cc_final: 0.7253 (m-80) REVERT: C 266 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.7767 (mmm160) REVERT: C 296 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6655 (mmm) REVERT: C 344 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.7159 (ttm-80) REVERT: C 347 LYS cc_start: 0.8002 (ttmm) cc_final: 0.7669 (tmtm) REVERT: C 430 LYS cc_start: 0.8239 (tmtm) cc_final: 0.7883 (tmmt) REVERT: D 140 LYS cc_start: 0.7609 (ttmm) cc_final: 0.7073 (mptt) REVERT: D 286 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7058 (tt0) REVERT: E 198 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7179 (ptmm) outliers start: 39 outliers final: 18 residues processed: 140 average time/residue: 0.7028 time to fit residues: 104.1827 Evaluate side-chains 127 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 126 MET 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 407 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 45 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.0870 chunk 88 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 143 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN ** 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 = 0.4303 r_free = 0.4303 target = 0.203988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.152075 restraints weight = 9296.452| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.26 r_work: 0.3474 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2222 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= 0.128 Angle : 0.583 14.265 12434 Z= 0.283 Chirality : 0.048 0.503 1426 Planarity : 0.006 0.154 1590 Dihedral : 9.694 94.173 1318 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.73 % Favored : 95.10 % Rotamer: Outliers : 3.64 % Allowed : 19.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.25), residues: 1142 helix: 1.18 (0.24), residues: 466 sheet: 1.20 (0.54), residues: 91 loop : -0.04 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 344 TYR 0.008 0.001 TYR C 205 PHE 0.014 0.001 PHE E 177 TRP 0.007 0.001 TRP D 473 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9197) covalent geometry : angle 0.58311 (12434) hydrogen bonds : bond 0.03199 ( 392) hydrogen bonds : angle 4.18112 ( 1119) metal coordination : bond 0.00184 ( 6) Misc. bond : bond 0.00065 ( 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 142 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: B 82 GLN cc_start: 0.7416 (mt0) cc_final: 0.7071 (mp10) REVERT: B 176 GLN cc_start: 0.7545 (mt0) cc_final: 0.7253 (mt0) REVERT: B 209 LYS cc_start: 0.7349 (tttm) cc_final: 0.7126 (pttm) REVERT: C 137 GLU cc_start: 0.7784 (tp30) cc_final: 0.7537 (mt-10) REVERT: C 140 LYS cc_start: 0.7614 (tptt) cc_final: 0.7274 (mtmm) REVERT: C 146 TYR cc_start: 0.7528 (t80) cc_final: 0.7196 (m-80) REVERT: C 266 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.7764 (mmm160) REVERT: C 296 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6615 (mmm) REVERT: C 344 ARG cc_start: 0.7701 (ttm-80) cc_final: 0.7175 (ttm-80) REVERT: C 347 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7707 (tmtm) REVERT: C 430 LYS cc_start: 0.8219 (tmtm) cc_final: 0.7879 (tmmt) REVERT: D 140 LYS cc_start: 0.7602 (ttmm) cc_final: 0.7048 (mptt) REVERT: D 286 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7046 (tt0) REVERT: E 189 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.5856 (mtp180) REVERT: E 198 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7209 (ptmm) outliers start: 36 outliers final: 16 residues processed: 131 average time/residue: 0.7410 time to fit residues: 102.5826 Evaluate side-chains 121 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 215 VAL Chi-restraints excluded: chain C residue 126 MET 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 469 SER Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain E residue 189 ARG Chi-restraints excluded: chain E residue 198 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 0.0010 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 76 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 143 ASN B 152 GLN B 170 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.205479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.148651 restraints weight = 9475.534| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.10 r_work: 0.3503 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 9205 Z= 0.116 Angle : 0.567 13.662 12434 Z= 0.276 Chirality : 0.047 0.461 1426 Planarity : 0.005 0.152 1590 Dihedral : 9.513 92.094 1318 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.47 % Favored : 95.36 % Rotamer: Outliers : 3.84 % Allowed : 19.21 % Favored : 76.95 % 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 aren not related in a simple way. whole: 0.81 (0.25), residues: 1142 helix: 1.17 (0.24), residues: 474 sheet: 1.20 (0.54), residues: 91 loop : -0.02 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 311 TYR 0.008 0.001 TYR D 350 PHE 0.015 0.001 PHE E 177 TRP 0.007 0.001 TRP D 482 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9197) covalent geometry : angle 0.56669 (12434) hydrogen bonds : bond 0.03060 ( 392) hydrogen bonds : angle 4.13003 ( 1119) metal coordination : bond 0.00152 ( 6) Misc. bond : bond 0.00048 ( 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 145 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: B 82 GLN cc_start: 0.7336 (mt0) cc_final: 0.6945 (mp10) REVERT: B 176 GLN cc_start: 0.7596 (mt0) cc_final: 0.7279 (mt0) REVERT: B 209 LYS cc_start: 0.7339 (tttm) cc_final: 0.6842 (ptmm) REVERT: C 137 GLU cc_start: 0.7912 (tp30) cc_final: 0.7538 (mt-10) REVERT: C 140 LYS cc_start: 0.7624 (tptt) cc_final: 0.7232 (mtmm) REVERT: C 146 TYR cc_start: 0.7644 (t80) cc_final: 0.7089 (m-80) REVERT: C 266 ARG cc_start: 0.8526 (mtm-85) cc_final: 0.7736 (mmm160) REVERT: C 296 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6750 (mmm) REVERT: C 344 ARG cc_start: 0.7714 (ttm-80) cc_final: 0.6964 (ttm-80) REVERT: C 347 LYS cc_start: 0.8103 (ttmm) cc_final: 0.7617 (tmtm) REVERT: C 430 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7911 (tmmt) REVERT: C 462 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8459 (mp0) REVERT: D 140 LYS cc_start: 0.7640 (ttmm) cc_final: 0.7016 (mptt) REVERT: D 286 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7135 (tt0) REVERT: E 72 LYS cc_start: 0.7533 (ttmt) cc_final: 0.7002 (tppt) REVERT: E 189 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.5849 (mtp180) REVERT: E 198 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7222 (ptmm) outliers start: 38 outliers final: 18 residues processed: 132 average time/residue: 0.7034 time to fit residues: 98.1198 Evaluate side-chains 127 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 430 LYS Chi-restraints excluded: chain C residue 462 GLU 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 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 80 GLN Chi-restraints excluded: chain E residue 141 VAL 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 55 optimal weight: 5.9990 chunk 29 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** 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 = 0.4305 r_free = 0.4305 target = 0.204689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.152939 restraints weight = 9392.989| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.99 r_work: 0.3470 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 9205 Z= 0.129 Angle : 0.588 13.269 12434 Z= 0.286 Chirality : 0.049 0.497 1426 Planarity : 0.005 0.150 1590 Dihedral : 9.505 93.533 1317 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.55 % Favored : 95.27 % Rotamer: Outliers : 3.13 % Allowed : 19.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.25), residues: 1142 helix: 1.11 (0.24), residues: 474 sheet: 1.17 (0.54), residues: 91 loop : -0.02 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 344 TYR 0.008 0.001 TYR C 205 PHE 0.016 0.001 PHE E 177 TRP 0.006 0.001 TRP D 473 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9197) covalent geometry : angle 0.58844 (12434) hydrogen bonds : bond 0.03164 ( 392) hydrogen bonds : angle 4.17803 ( 1119) metal coordination : bond 0.00188 ( 6) Misc. bond : bond 0.00063 ( 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 134 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.376 Fit side-chains REVERT: B 82 GLN cc_start: 0.7356 (mt0) cc_final: 0.6997 (mp10) REVERT: B 176 GLN cc_start: 0.7626 (mt0) cc_final: 0.7263 (mt0) REVERT: B 209 LYS cc_start: 0.7361 (tttm) cc_final: 0.6910 (ptmm) REVERT: C 137 GLU cc_start: 0.7941 (tp30) cc_final: 0.7576 (mt-10) REVERT: C 140 LYS cc_start: 0.7675 (tptt) cc_final: 0.7287 (mtmm) REVERT: C 146 TYR cc_start: 0.7703 (t80) cc_final: 0.7081 (m-80) REVERT: C 266 ARG cc_start: 0.8545 (mtm-85) cc_final: 0.7752 (mmm160) REVERT: C 296 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6849 (mmm) REVERT: C 344 ARG cc_start: 0.7752 (ttm-80) cc_final: 0.7000 (ttm-80) REVERT: C 347 LYS cc_start: 0.8148 (ttmm) cc_final: 0.7650 (tmtm) REVERT: C 430 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7943 (tmmt) REVERT: D 286 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7178 (tt0) REVERT: E 72 LYS cc_start: 0.7572 (ttmt) cc_final: 0.7038 (tppt) REVERT: E 189 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.5832 (mtp180) REVERT: E 198 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7241 (ptmm) outliers start: 31 outliers final: 17 residues processed: 123 average time/residue: 0.7281 time to fit residues: 94.7512 Evaluate side-chains 123 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 430 LYS 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 78 LEU 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 12 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN E 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.203982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.153147 restraints weight = 9442.619| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.88 r_work: 0.3460 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2512 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= 0.143 Angle : 0.609 12.951 12434 Z= 0.295 Chirality : 0.050 0.539 1426 Planarity : 0.005 0.149 1590 Dihedral : 9.668 95.799 1317 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.47 % Favored : 95.36 % Rotamer: Outliers : 2.83 % Allowed : 20.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.25), residues: 1142 helix: 1.04 (0.24), residues: 474 sheet: 1.12 (0.55), residues: 91 loop : -0.03 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 190 TYR 0.008 0.001 TYR D 350 PHE 0.017 0.001 PHE E 177 TRP 0.007 0.001 TRP D 482 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9197) covalent geometry : angle 0.60921 (12434) hydrogen bonds : bond 0.03270 ( 392) hydrogen bonds : angle 4.24446 ( 1119) metal coordination : bond 0.00223 ( 6) Misc. bond : bond 0.00082 ( 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 129 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.364 Fit side-chains REVERT: B 82 GLN cc_start: 0.7338 (mt0) cc_final: 0.7000 (mp10) REVERT: B 176 GLN cc_start: 0.7640 (mt0) cc_final: 0.7246 (mt0) REVERT: B 209 LYS cc_start: 0.7409 (tttm) cc_final: 0.6956 (ptmm) REVERT: C 137 GLU cc_start: 0.7959 (tp30) cc_final: 0.7618 (mt-10) REVERT: C 140 LYS cc_start: 0.7708 (tptt) cc_final: 0.7323 (mtmm) REVERT: C 146 TYR cc_start: 0.7716 (t80) cc_final: 0.7150 (m-80) REVERT: C 266 ARG cc_start: 0.8575 (mtm-85) cc_final: 0.7837 (mmm160) REVERT: C 296 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6920 (mmm) REVERT: C 344 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7083 (ttm-80) REVERT: C 347 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7742 (tmtm) REVERT: C 430 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8012 (tmmt) REVERT: D 140 LYS cc_start: 0.7723 (ttmm) cc_final: 0.7322 (mptt) REVERT: D 286 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: E 189 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.5752 (mtp180) outliers start: 28 outliers final: 17 residues processed: 117 average time/residue: 0.7116 time to fit residues: 88.3771 Evaluate side-chains 118 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 430 LYS 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 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 78 LEU 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 58 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN E 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.205647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.155192 restraints weight = 9426.776| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.26 r_work: 0.3494 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 9205 Z= 0.118 Angle : 0.581 12.528 12434 Z= 0.284 Chirality : 0.047 0.450 1426 Planarity : 0.005 0.147 1590 Dihedral : 9.507 92.800 1317 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.29 % Favored : 95.53 % Rotamer: Outliers : 2.73 % Allowed : 20.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.25), residues: 1142 helix: 1.06 (0.24), residues: 474 sheet: 1.16 (0.55), residues: 91 loop : 0.01 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 344 TYR 0.009 0.001 TYR D 350 PHE 0.017 0.001 PHE E 177 TRP 0.006 0.001 TRP D 473 HIS 0.005 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9197) covalent geometry : angle 0.58068 (12434) hydrogen bonds : bond 0.03071 ( 392) hydrogen bonds : angle 4.16514 ( 1119) metal coordination : bond 0.00157 ( 6) Misc. bond : bond 0.00047 ( 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 126 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.370 Fit side-chains REVERT: B 82 GLN cc_start: 0.7365 (mt0) cc_final: 0.7039 (mp10) REVERT: B 176 GLN cc_start: 0.7700 (mt0) cc_final: 0.7324 (mt0) REVERT: B 209 LYS cc_start: 0.7384 (tttm) cc_final: 0.6955 (ptmm) REVERT: C 137 GLU cc_start: 0.7946 (tp30) cc_final: 0.7630 (mt-10) REVERT: C 140 LYS cc_start: 0.7712 (tptt) cc_final: 0.7312 (mtmm) REVERT: C 146 TYR cc_start: 0.7692 (t80) cc_final: 0.7154 (m-80) REVERT: C 266 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.7854 (mmm160) REVERT: C 296 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6871 (mmm) REVERT: C 344 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7077 (ttm-80) REVERT: C 347 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7741 (tmtm) REVERT: C 430 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7997 (tmmt) REVERT: D 140 LYS cc_start: 0.7678 (ttmm) cc_final: 0.7285 (mptt) REVERT: D 286 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: E 189 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.5826 (mtp180) REVERT: E 198 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7241 (ptmm) outliers start: 27 outliers final: 15 residues processed: 115 average time/residue: 0.7237 time to fit residues: 88.2404 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 : 0.372 ------------------------------------------------------------------------------- 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 430 LYS 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 407 SER Chi-restraints excluded: chain D residue 410 MET 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 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 23 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 50 optimal weight: 0.0370 chunk 97 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.6662 ------------------------------------------------------------------------------- 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 ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN E 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.205260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.154832 restraints weight = 9328.994| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.38 r_work: 0.3490 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 9205 Z= 0.124 Angle : 0.590 12.261 12434 Z= 0.289 Chirality : 0.048 0.466 1426 Planarity : 0.005 0.146 1590 Dihedral : 9.447 92.698 1317 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.47 % Favored : 95.36 % Rotamer: Outliers : 2.43 % Allowed : 21.03 % Favored : 76.54 % 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 aren not related in a simple way. whole: 0.71 (0.25), residues: 1142 helix: 1.02 (0.24), residues: 474 sheet: 1.11 (0.55), residues: 91 loop : 0.01 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 311 TYR 0.008 0.001 TYR C 205 PHE 0.017 0.001 PHE E 177 TRP 0.006 0.001 TRP D 473 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9197) covalent geometry : angle 0.58991 (12434) hydrogen bonds : bond 0.03179 ( 392) hydrogen bonds : angle 4.18327 ( 1119) metal coordination : bond 0.00173 ( 6) Misc. bond : bond 0.00053 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4040.36 seconds wall clock time: 69 minutes 42.90 seconds (4182.90 seconds total)