Starting phenix.real_space_refine on Thu Mar 13 04:07:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ej0_31147/03_2025/7ej0_31147.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ej0_31147/03_2025/7ej0_31147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ej0_31147/03_2025/7ej0_31147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ej0_31147/03_2025/7ej0_31147.map" model { file = "/net/cci-nas-00/data/ceres_data/7ej0_31147/03_2025/7ej0_31147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ej0_31147/03_2025/7ej0_31147.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.024 sd= 0.466 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5486 2.51 5 N 1462 2.21 5 O 1593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8600 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1715 Classifications: {'peptide': 217} Link IDs: {'CIS': 7, 'PTRANS': 4, 'TRANS': 205} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2564 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PTRANS': 5, 'TRANS': 326} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 48} Chain: "H" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1794 Classifications: {'peptide': 233} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2097 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 248} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'E5E': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 5.59, per 1000 atoms: 0.65 Number of scatterers: 8600 At special positions: 0 Unit cell: (90.95, 120.7, 124.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1593 8.00 N 1462 7.00 C 5486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 121 " - pdb=" SG CYS R 203 " distance=1.82 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.0 seconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 14 sheets defined 34.1% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.604A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.931A pdb=" N LYS A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.940A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 removed outlier: 4.521A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'R' and resid 47 through 74 Processing helix chain 'R' and resid 83 through 108 removed outlier: 4.301A pdb=" N LEU R 87 " --> pdb=" O GLN R 83 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU R 96 " --> pdb=" O SER R 92 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA R 98 " --> pdb=" O ASP R 94 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR R 99 " --> pdb=" O ILE R 95 " (cutoff:3.500A) Proline residue: R 103 - end of helix Processing helix chain 'R' and resid 121 through 151 removed outlier: 3.605A pdb=" N SER R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE R 136 " --> pdb=" O CYS R 132 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N CYS R 140 " --> pdb=" O ILE R 136 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA R 141 " --> pdb=" O VAL R 137 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER R 143 " --> pdb=" O LEU R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 158 removed outlier: 4.044A pdb=" N LEU R 158 " --> pdb=" O ILE R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 181 Processing helix chain 'R' and resid 208 through 220 removed outlier: 3.891A pdb=" N ILE R 213 " --> pdb=" O LYS R 209 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER R 214 " --> pdb=" O TRP R 210 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE R 217 " --> pdb=" O ILE R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 241 removed outlier: 3.936A pdb=" N LEU R 225 " --> pdb=" O PHE R 221 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG R 241 " --> pdb=" O ILE R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 380 through 412 removed outlier: 3.803A pdb=" N LYS R 385 " --> pdb=" O GLN R 381 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG R 386 " --> pdb=" O ASN R 382 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR R 388 " --> pdb=" O GLU R 384 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE R 389 " --> pdb=" O LYS R 385 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE R 398 " --> pdb=" O VAL R 394 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL R 399 " --> pdb=" O ILE R 395 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N CYS R 401 " --> pdb=" O VAL R 397 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TRP R 402 " --> pdb=" O PHE R 398 " (cutoff:3.500A) Proline residue: R 404 - end of helix Processing helix chain 'R' and resid 422 through 443 removed outlier: 3.585A pdb=" N TRP R 428 " --> pdb=" O LYS R 424 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE R 429 " --> pdb=" O PHE R 425 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR R 431 " --> pdb=" O PHE R 427 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER R 434 " --> pdb=" O GLY R 430 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN R 437 " --> pdb=" O ASN R 433 " (cutoff:3.500A) Proline residue: R 438 - end of helix removed outlier: 3.537A pdb=" N THR R 442 " --> pdb=" O PRO R 438 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 457 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.608A pdb=" N VAL A 34 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.476A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.634A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.107A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 153 removed outlier: 6.477A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.831A pdb=" N ASP B 170 " --> pdb=" O GLN B 175 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.975A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 232 Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.719A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.648A pdb=" N THR H 69 " --> pdb=" O GLN H 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.786A pdb=" N TYR H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'H' and resid 134 through 135 removed outlier: 3.828A pdb=" N VAL H 135 " --> pdb=" O LYS H 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'H' and resid 174 through 178 removed outlier: 6.686A pdb=" N TRP H 164 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR H 178 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU H 162 " --> pdb=" O TYR H 178 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.60 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1380 1.29 - 1.42: 2378 1.42 - 1.55: 4936 1.55 - 1.68: 5 1.68 - 1.81: 81 Bond restraints: 8780 Sorted by residual: bond pdb=" CA ASN R 437 " pdb=" C ASN R 437 " ideal model delta sigma weight residual 1.522 1.406 0.116 1.29e-02 6.01e+03 8.02e+01 bond pdb=" N PRO R 223 " pdb=" CD PRO R 223 " ideal model delta sigma weight residual 1.473 1.360 0.113 1.40e-02 5.10e+03 6.49e+01 bond pdb=" N ARG A 349 " pdb=" CA ARG A 349 " ideal model delta sigma weight residual 1.459 1.363 0.096 1.25e-02 6.40e+03 5.89e+01 bond pdb=" CA LEU R 125 " pdb=" C LEU R 125 " ideal model delta sigma weight residual 1.524 1.429 0.095 1.27e-02 6.20e+03 5.54e+01 bond pdb=" C SER R 135 " pdb=" O SER R 135 " ideal model delta sigma weight residual 1.236 1.155 0.082 1.15e-02 7.56e+03 5.03e+01 ... (remaining 8775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 11751 4.68 - 9.36: 128 9.36 - 14.03: 13 14.03 - 18.71: 1 18.71 - 23.39: 1 Bond angle restraints: 11894 Sorted by residual: angle pdb=" N LEU R 436 " pdb=" CA LEU R 436 " pdb=" C LEU R 436 " ideal model delta sigma weight residual 111.36 126.23 -14.87 1.09e+00 8.42e-01 1.86e+02 angle pdb=" N CYS R 224 " pdb=" CA CYS R 224 " pdb=" C CYS R 224 " ideal model delta sigma weight residual 111.36 98.77 12.59 1.09e+00 8.42e-01 1.33e+02 angle pdb=" N LEU A 348 " pdb=" CA LEU A 348 " pdb=" C LEU A 348 " ideal model delta sigma weight residual 111.71 98.51 13.20 1.15e+00 7.56e-01 1.32e+02 angle pdb=" N THR R 442 " pdb=" CA THR R 442 " pdb=" C THR R 442 " ideal model delta sigma weight residual 112.23 124.38 -12.15 1.26e+00 6.30e-01 9.30e+01 angle pdb=" N ALA R 238 " pdb=" CA ALA R 238 " pdb=" C ALA R 238 " ideal model delta sigma weight residual 113.16 103.92 9.24 1.24e+00 6.50e-01 5.55e+01 ... (remaining 11889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 4686 17.55 - 35.11: 400 35.11 - 52.66: 88 52.66 - 70.21: 11 70.21 - 87.77: 8 Dihedral angle restraints: 5193 sinusoidal: 2014 harmonic: 3179 Sorted by residual: dihedral pdb=" C TYR R 231 " pdb=" N TYR R 231 " pdb=" CA TYR R 231 " pdb=" CB TYR R 231 " ideal model delta harmonic sigma weight residual -122.60 -140.36 17.76 0 2.50e+00 1.60e-01 5.05e+01 dihedral pdb=" N TYR R 231 " pdb=" C TYR R 231 " pdb=" CA TYR R 231 " pdb=" CB TYR R 231 " ideal model delta harmonic sigma weight residual 122.80 138.80 -16.00 0 2.50e+00 1.60e-01 4.09e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 146.60 -53.60 1 1.00e+01 1.00e-02 3.90e+01 ... (remaining 5190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 1312 0.167 - 0.334: 26 0.334 - 0.501: 8 0.501 - 0.668: 5 0.668 - 0.836: 1 Chirality restraints: 1352 Sorted by residual: chirality pdb=" CA TYR R 231 " pdb=" N TYR R 231 " pdb=" C TYR R 231 " pdb=" CB TYR R 231 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.75e+01 chirality pdb=" CA ARG A 349 " pdb=" N ARG A 349 " pdb=" C ARG A 349 " pdb=" CB ARG A 349 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" CA PRO R 223 " pdb=" N PRO R 223 " pdb=" C PRO R 223 " pdb=" CB PRO R 223 " both_signs ideal model delta sigma weight residual False 2.72 2.17 0.55 2.00e-01 2.50e+01 7.56e+00 ... (remaining 1349 not shown) Planarity restraints: 1501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA R 222 " -0.084 5.00e-02 4.00e+02 1.45e-01 3.35e+01 pdb=" N PRO R 223 " 0.251 5.00e-02 4.00e+02 pdb=" CA PRO R 223 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO R 223 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 226 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C ILE R 226 " 0.067 2.00e-02 2.50e+03 pdb=" O ILE R 226 " -0.025 2.00e-02 2.50e+03 pdb=" N MET R 227 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 142 " 0.019 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C ILE R 142 " -0.067 2.00e-02 2.50e+03 pdb=" O ILE R 142 " 0.025 2.00e-02 2.50e+03 pdb=" N SER R 143 " 0.022 2.00e-02 2.50e+03 ... (remaining 1498 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 19 2.37 - 3.00: 4886 3.00 - 3.63: 12685 3.63 - 4.27: 17772 4.27 - 4.90: 29873 Nonbonded interactions: 65235 Sorted by model distance: nonbonded pdb=" O LEU R 422 " pdb=" N PHE R 425 " model vdw 1.736 3.120 nonbonded pdb=" OD1 ASP R 94 " pdb=" OG SER R 434 " model vdw 2.150 3.040 nonbonded pdb=" O THR R 133 " pdb=" CG2 VAL R 137 " model vdw 2.157 3.460 nonbonded pdb=" O HIS R 446 " pdb=" C ASP R 447 " model vdw 2.162 3.270 nonbonded pdb=" OG SER R 89 " pdb=" NE2 HIS R 138 " model vdw 2.195 3.120 ... (remaining 65230 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 2.720 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.510 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.009 0.116 8780 Z= 0.594 Angle : 1.116 23.392 11894 Z= 0.716 Chirality : 0.075 0.836 1352 Planarity : 0.006 0.145 1501 Dihedral : 13.818 87.768 3131 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.43 % Allowed : 1.93 % Favored : 97.65 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.25), residues: 1078 helix: 0.48 (0.30), residues: 333 sheet: 0.22 (0.34), residues: 231 loop : -1.87 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 428 HIS 0.004 0.001 HIS R 138 PHE 0.038 0.002 PHE R 220 TYR 0.033 0.002 TYR R 431 ARG 0.006 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 277 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.8024 (tppp) cc_final: 0.7765 (ttmt) REVERT: G 46 LYS cc_start: 0.8841 (tptp) cc_final: 0.8471 (tppt) REVERT: R 208 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7545 (mt0) REVERT: R 425 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8572 (m-10) REVERT: R 445 ASN cc_start: 0.7983 (t0) cc_final: 0.7774 (t0) outliers start: 4 outliers final: 3 residues processed: 280 average time/residue: 0.2095 time to fit residues: 81.6420 Evaluate side-chains 202 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 198 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 423 PHE Chi-restraints excluded: chain R residue 425 PHE Chi-restraints excluded: chain R residue 436 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 347 ASN B 13 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN H 157 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.125700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.100852 restraints weight = 18208.289| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.62 r_work: 0.3327 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8780 Z= 0.296 Angle : 0.742 10.421 11894 Z= 0.386 Chirality : 0.048 0.195 1352 Planarity : 0.005 0.076 1501 Dihedral : 5.935 53.255 1202 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.14 % Allowed : 15.19 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.25), residues: 1078 helix: 0.96 (0.28), residues: 346 sheet: -0.08 (0.33), residues: 246 loop : -1.93 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 428 HIS 0.007 0.001 HIS B 311 PHE 0.021 0.002 PHE R 426 TYR 0.014 0.001 TYR R 441 ARG 0.006 0.001 ARG R 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.949 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 53 MET cc_start: 0.7217 (ppp) cc_final: 0.6481 (pmm) REVERT: A 291 TYR cc_start: 0.7544 (t80) cc_final: 0.6960 (t80) REVERT: A 349 ARG cc_start: 0.8410 (tpp80) cc_final: 0.7819 (ttm110) REVERT: B 169 TRP cc_start: 0.8011 (m-10) cc_final: 0.7643 (m-10) REVERT: B 262 MET cc_start: 0.9007 (mmm) cc_final: 0.8764 (mmp) REVERT: B 312 ASP cc_start: 0.6920 (t0) cc_final: 0.6699 (t0) REVERT: G 27 ARG cc_start: 0.6823 (ptt-90) cc_final: 0.6359 (ptt90) REVERT: G 46 LYS cc_start: 0.8921 (tptp) cc_final: 0.8567 (tppt) REVERT: H 68 PHE cc_start: 0.7936 (m-10) cc_final: 0.7689 (m-10) REVERT: R 155 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8651 (tp30) REVERT: R 206 ASN cc_start: 0.8266 (t0) cc_final: 0.7987 (t0) REVERT: R 207 ASP cc_start: 0.8725 (p0) cc_final: 0.8058 (t0) REVERT: R 236 GLN cc_start: 0.8847 (mm110) cc_final: 0.8373 (mt0) REVERT: R 240 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.8307 (mmp80) REVERT: R 445 ASN cc_start: 0.8175 (t0) cc_final: 0.7895 (t0) outliers start: 20 outliers final: 12 residues processed: 224 average time/residue: 0.1916 time to fit residues: 59.8495 Evaluate side-chains 202 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 399 VAL Chi-restraints excluded: chain R residue 400 VAL Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN B 13 GLN B 293 ASN R 66 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.122116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096898 restraints weight = 18746.820| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.65 r_work: 0.3263 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8780 Z= 0.335 Angle : 0.726 9.573 11894 Z= 0.383 Chirality : 0.047 0.183 1352 Planarity : 0.004 0.058 1501 Dihedral : 5.816 53.450 1196 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.74 % Allowed : 18.07 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 1078 helix: 1.17 (0.29), residues: 347 sheet: -0.21 (0.33), residues: 243 loop : -2.09 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 428 HIS 0.009 0.001 HIS B 311 PHE 0.019 0.002 PHE R 181 TYR 0.011 0.001 TYR H 178 ARG 0.005 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 1.013 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 53 MET cc_start: 0.7313 (ppp) cc_final: 0.6596 (pmm) REVERT: A 349 ARG cc_start: 0.8548 (tpp80) cc_final: 0.7937 (ttm110) REVERT: B 59 TYR cc_start: 0.8788 (m-80) cc_final: 0.8583 (m-80) REVERT: B 175 GLN cc_start: 0.8536 (pm20) cc_final: 0.7898 (pm20) REVERT: B 259 GLN cc_start: 0.7339 (mm-40) cc_final: 0.6688 (mm110) REVERT: B 312 ASP cc_start: 0.7358 (t0) cc_final: 0.7138 (t0) REVERT: G 27 ARG cc_start: 0.7176 (ptt-90) cc_final: 0.6201 (ptt90) REVERT: G 46 LYS cc_start: 0.8868 (tptp) cc_final: 0.8520 (tppt) REVERT: H 1 ASP cc_start: 0.8248 (m-30) cc_final: 0.7899 (t0) REVERT: H 141 GLU cc_start: 0.8280 (tp30) cc_final: 0.7953 (tp30) REVERT: R 155 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8667 (tp30) REVERT: R 206 ASN cc_start: 0.8238 (t0) cc_final: 0.7943 (t0) REVERT: R 207 ASP cc_start: 0.8676 (p0) cc_final: 0.8099 (t0) REVERT: R 236 GLN cc_start: 0.8815 (mm110) cc_final: 0.8400 (mt0) REVERT: R 240 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8363 (mmp80) REVERT: R 445 ASN cc_start: 0.8153 (t0) cc_final: 0.7898 (t0) outliers start: 35 outliers final: 22 residues processed: 220 average time/residue: 0.1878 time to fit residues: 57.9855 Evaluate side-chains 202 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 399 VAL Chi-restraints excluded: chain R residue 400 VAL Chi-restraints excluded: chain R residue 442 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.118135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.092758 restraints weight = 18565.678| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.62 r_work: 0.3201 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8780 Z= 0.418 Angle : 0.781 11.312 11894 Z= 0.413 Chirality : 0.049 0.193 1352 Planarity : 0.005 0.051 1501 Dihedral : 6.225 56.196 1196 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 5.99 % Allowed : 18.40 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.25), residues: 1078 helix: 1.11 (0.28), residues: 351 sheet: -0.37 (0.34), residues: 241 loop : -2.31 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 339 HIS 0.009 0.002 HIS B 311 PHE 0.021 0.002 PHE R 181 TYR 0.014 0.002 TYR H 178 ARG 0.006 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 182 time to evaluate : 0.906 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 206 ARG cc_start: 0.8973 (mmm-85) cc_final: 0.8757 (mmm160) REVERT: A 291 TYR cc_start: 0.7429 (t80) cc_final: 0.6880 (t80) REVERT: A 313 ARG cc_start: 0.8968 (mmt90) cc_final: 0.8753 (mmm160) REVERT: A 349 ARG cc_start: 0.8608 (tpp80) cc_final: 0.7995 (ttm110) REVERT: B 312 ASP cc_start: 0.7714 (t0) cc_final: 0.7461 (t0) REVERT: G 27 ARG cc_start: 0.7385 (ptt-90) cc_final: 0.6561 (ptt90) REVERT: G 46 LYS cc_start: 0.8864 (tptp) cc_final: 0.8488 (tppt) REVERT: H 1 ASP cc_start: 0.8268 (m-30) cc_final: 0.7753 (t0) REVERT: H 141 GLU cc_start: 0.8300 (tp30) cc_final: 0.8031 (tp30) REVERT: R 106 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9104 (mm) REVERT: R 155 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8716 (tp30) REVERT: R 166 LYS cc_start: 0.8088 (mttm) cc_final: 0.7845 (mmtt) REVERT: R 206 ASN cc_start: 0.8209 (t0) cc_final: 0.7940 (t0) REVERT: R 207 ASP cc_start: 0.8607 (p0) cc_final: 0.8117 (t0) REVERT: R 236 GLN cc_start: 0.8808 (mm110) cc_final: 0.8410 (mt0) REVERT: R 240 ARG cc_start: 0.8706 (mmm-85) cc_final: 0.8383 (mmp80) REVERT: R 435 SER cc_start: 0.9263 (t) cc_final: 0.8775 (p) REVERT: R 445 ASN cc_start: 0.8263 (t0) cc_final: 0.8007 (t0) REVERT: R 446 HIS cc_start: 0.8526 (p90) cc_final: 0.8231 (p90) outliers start: 56 outliers final: 41 residues processed: 216 average time/residue: 0.1865 time to fit residues: 56.5864 Evaluate side-chains 217 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 399 VAL Chi-restraints excluded: chain R residue 400 VAL Chi-restraints excluded: chain R residue 439 VAL Chi-restraints excluded: chain R residue 440 ILE Chi-restraints excluded: chain R residue 442 THR Chi-restraints excluded: chain R residue 453 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 0.0060 chunk 97 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.121760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.096643 restraints weight = 18207.160| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.58 r_work: 0.3268 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8780 Z= 0.212 Angle : 0.669 8.775 11894 Z= 0.353 Chirality : 0.045 0.177 1352 Planarity : 0.004 0.042 1501 Dihedral : 5.950 55.692 1196 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.85 % Allowed : 22.46 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.25), residues: 1078 helix: 1.31 (0.28), residues: 348 sheet: -0.36 (0.34), residues: 242 loop : -2.27 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.008 0.001 HIS B 311 PHE 0.029 0.001 PHE B 235 TYR 0.008 0.001 TYR R 409 ARG 0.003 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 0.889 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 270 ASN cc_start: 0.8572 (t0) cc_final: 0.8336 (t0) REVERT: A 291 TYR cc_start: 0.7333 (t80) cc_final: 0.6845 (t80) REVERT: A 313 ARG cc_start: 0.8900 (mmt90) cc_final: 0.8689 (mmm160) REVERT: A 349 ARG cc_start: 0.8605 (tpp80) cc_final: 0.7965 (ttm110) REVERT: B 59 TYR cc_start: 0.8709 (m-80) cc_final: 0.8421 (m-80) REVERT: B 175 GLN cc_start: 0.8511 (pm20) cc_final: 0.7813 (pm20) REVERT: B 259 GLN cc_start: 0.7293 (mm-40) cc_final: 0.6887 (mm110) REVERT: G 46 LYS cc_start: 0.8863 (tptp) cc_final: 0.8484 (tppt) REVERT: H 1 ASP cc_start: 0.8318 (m-30) cc_final: 0.7798 (t0) REVERT: H 141 GLU cc_start: 0.8311 (tp30) cc_final: 0.8014 (tp30) REVERT: H 208 GLU cc_start: 0.8289 (pp20) cc_final: 0.8057 (pp20) REVERT: R 106 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8988 (mm) REVERT: R 155 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8692 (tp30) REVERT: R 206 ASN cc_start: 0.8188 (t0) cc_final: 0.7903 (t0) REVERT: R 207 ASP cc_start: 0.8577 (p0) cc_final: 0.8113 (t0) REVERT: R 233 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8487 (tpt90) REVERT: R 236 GLN cc_start: 0.8747 (mm110) cc_final: 0.8403 (mt0) REVERT: R 240 ARG cc_start: 0.8644 (mmm-85) cc_final: 0.8317 (mmp80) REVERT: R 435 SER cc_start: 0.9244 (t) cc_final: 0.8757 (p) REVERT: R 445 ASN cc_start: 0.8151 (t0) cc_final: 0.7890 (t0) outliers start: 36 outliers final: 25 residues processed: 226 average time/residue: 0.1900 time to fit residues: 60.0769 Evaluate side-chains 214 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 440 ILE Chi-restraints excluded: chain R residue 442 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 0.0060 chunk 88 optimal weight: 7.9990 chunk 104 optimal weight: 0.1980 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 42 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 13 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.122982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.097744 restraints weight = 17972.709| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.59 r_work: 0.3301 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8780 Z= 0.180 Angle : 0.653 11.539 11894 Z= 0.341 Chirality : 0.044 0.173 1352 Planarity : 0.004 0.040 1501 Dihedral : 5.818 56.222 1196 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.21 % Allowed : 24.17 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.25), residues: 1078 helix: 1.37 (0.28), residues: 350 sheet: -0.31 (0.33), residues: 246 loop : -2.22 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 47 HIS 0.003 0.001 HIS H 220 PHE 0.036 0.001 PHE B 235 TYR 0.009 0.001 TYR G 40 ARG 0.003 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.886 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.9022 (tp30) cc_final: 0.8584 (tp30) REVERT: A 270 ASN cc_start: 0.8596 (t0) cc_final: 0.8363 (t0) REVERT: A 313 ARG cc_start: 0.8892 (mmt90) cc_final: 0.8673 (mmm160) REVERT: A 349 ARG cc_start: 0.8598 (tpp80) cc_final: 0.8011 (ttm110) REVERT: B 59 TYR cc_start: 0.8729 (m-80) cc_final: 0.8495 (m-80) REVERT: B 175 GLN cc_start: 0.8600 (pm20) cc_final: 0.7923 (pm20) REVERT: B 259 GLN cc_start: 0.7351 (mm-40) cc_final: 0.6759 (mm110) REVERT: B 262 MET cc_start: 0.9031 (mmm) cc_final: 0.8766 (mmm) REVERT: G 27 ARG cc_start: 0.6881 (ptt-90) cc_final: 0.6400 (ptt90) REVERT: G 46 LYS cc_start: 0.8867 (tptp) cc_final: 0.8472 (tppt) REVERT: H 1 ASP cc_start: 0.8328 (m-30) cc_final: 0.7796 (t0) REVERT: H 141 GLU cc_start: 0.8416 (tp30) cc_final: 0.8089 (tp30) REVERT: R 106 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8968 (mm) REVERT: R 155 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8667 (tp30) REVERT: R 206 ASN cc_start: 0.8202 (t0) cc_final: 0.7921 (t0) REVERT: R 207 ASP cc_start: 0.8534 (p0) cc_final: 0.8100 (t0) REVERT: R 236 GLN cc_start: 0.8751 (mm110) cc_final: 0.8545 (mt0) REVERT: R 240 ARG cc_start: 0.8649 (mmm-85) cc_final: 0.8295 (mmp80) REVERT: R 435 SER cc_start: 0.9217 (t) cc_final: 0.8720 (p) REVERT: R 445 ASN cc_start: 0.8047 (t0) cc_final: 0.7788 (t0) outliers start: 30 outliers final: 19 residues processed: 227 average time/residue: 0.1830 time to fit residues: 58.0652 Evaluate side-chains 209 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 442 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 96 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.120127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.094814 restraints weight = 18455.222| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.61 r_work: 0.3250 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8780 Z= 0.264 Angle : 0.689 10.557 11894 Z= 0.362 Chirality : 0.046 0.182 1352 Planarity : 0.004 0.039 1501 Dihedral : 5.943 59.787 1194 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.96 % Allowed : 24.81 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.25), residues: 1078 helix: 1.41 (0.28), residues: 354 sheet: -0.40 (0.33), residues: 246 loop : -2.25 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 339 HIS 0.004 0.001 HIS H 220 PHE 0.037 0.002 PHE B 235 TYR 0.009 0.001 TYR H 178 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.978 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. REVERT: A 20 GLU cc_start: 0.9063 (tp30) cc_final: 0.8641 (tp30) REVERT: A 39 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7934 (tt) REVERT: A 270 ASN cc_start: 0.8622 (t0) cc_final: 0.8386 (t0) REVERT: A 291 TYR cc_start: 0.7347 (t80) cc_final: 0.6750 (t80) REVERT: A 313 ARG cc_start: 0.8920 (mmt90) cc_final: 0.8702 (mmm160) REVERT: A 349 ARG cc_start: 0.8605 (tpp80) cc_final: 0.8027 (ttm110) REVERT: B 59 TYR cc_start: 0.8768 (m-80) cc_final: 0.8407 (m-80) REVERT: B 175 GLN cc_start: 0.8642 (pm20) cc_final: 0.7959 (pm20) REVERT: B 259 GLN cc_start: 0.7389 (mm-40) cc_final: 0.6716 (mm110) REVERT: B 339 TRP cc_start: 0.8085 (OUTLIER) cc_final: 0.7884 (m-10) REVERT: G 27 ARG cc_start: 0.7090 (ptt-90) cc_final: 0.6390 (ptt90) REVERT: G 46 LYS cc_start: 0.8863 (tptp) cc_final: 0.8469 (tppt) REVERT: H 141 GLU cc_start: 0.8411 (tp30) cc_final: 0.8109 (tp30) REVERT: R 106 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8974 (mm) REVERT: R 155 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8698 (tp30) REVERT: R 166 LYS cc_start: 0.8005 (mttm) cc_final: 0.7756 (mmtt) REVERT: R 206 ASN cc_start: 0.8199 (t0) cc_final: 0.7926 (t0) REVERT: R 207 ASP cc_start: 0.8542 (p0) cc_final: 0.8191 (t0) REVERT: R 240 ARG cc_start: 0.8645 (mmm-85) cc_final: 0.8302 (mmp80) REVERT: R 416 CYS cc_start: 0.7868 (t) cc_final: 0.7016 (p) REVERT: R 435 SER cc_start: 0.9252 (t) cc_final: 0.8742 (p) REVERT: R 445 ASN cc_start: 0.8146 (t0) cc_final: 0.7924 (t0) outliers start: 37 outliers final: 29 residues processed: 216 average time/residue: 0.1950 time to fit residues: 58.9965 Evaluate side-chains 219 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 400 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 442 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 78 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.120562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.095130 restraints weight = 18529.183| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.63 r_work: 0.3254 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8780 Z= 0.234 Angle : 0.685 10.458 11894 Z= 0.356 Chirality : 0.045 0.180 1352 Planarity : 0.004 0.040 1501 Dihedral : 5.853 58.114 1194 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.28 % Allowed : 24.71 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.26), residues: 1078 helix: 1.53 (0.28), residues: 352 sheet: -0.36 (0.33), residues: 244 loop : -2.25 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 339 HIS 0.004 0.001 HIS B 311 PHE 0.043 0.001 PHE B 235 TYR 0.009 0.001 TYR H 178 ARG 0.003 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 1.043 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. REVERT: A 20 GLU cc_start: 0.9047 (tp30) cc_final: 0.8615 (tp30) REVERT: A 39 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7893 (tt) REVERT: A 270 ASN cc_start: 0.8621 (t0) cc_final: 0.8380 (t0) REVERT: A 291 TYR cc_start: 0.7315 (t80) cc_final: 0.6773 (t80) REVERT: A 313 ARG cc_start: 0.8916 (mmt90) cc_final: 0.8696 (mmm160) REVERT: A 349 ARG cc_start: 0.8587 (tpp80) cc_final: 0.8026 (ttm110) REVERT: B 175 GLN cc_start: 0.8629 (pm20) cc_final: 0.7860 (pm20) REVERT: B 259 GLN cc_start: 0.7422 (mm-40) cc_final: 0.6747 (mm110) REVERT: G 27 ARG cc_start: 0.7038 (ptt-90) cc_final: 0.6271 (ptt90) REVERT: G 46 LYS cc_start: 0.8879 (tptp) cc_final: 0.8484 (tppt) REVERT: H 141 GLU cc_start: 0.8377 (tp30) cc_final: 0.8063 (tp30) REVERT: R 106 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8948 (mm) REVERT: R 155 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8674 (tp30) REVERT: R 166 LYS cc_start: 0.7988 (mttm) cc_final: 0.7775 (mmtt) REVERT: R 206 ASN cc_start: 0.8188 (t0) cc_final: 0.7912 (t0) REVERT: R 207 ASP cc_start: 0.8528 (p0) cc_final: 0.8169 (t0) REVERT: R 416 CYS cc_start: 0.7916 (t) cc_final: 0.7122 (p) REVERT: R 445 ASN cc_start: 0.8083 (t0) cc_final: 0.7841 (t0) outliers start: 40 outliers final: 31 residues processed: 215 average time/residue: 0.1897 time to fit residues: 57.2531 Evaluate side-chains 218 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 400 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 442 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 0.0000 chunk 47 optimal weight: 0.5980 chunk 100 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.121095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.095455 restraints weight = 18387.297| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.63 r_work: 0.3267 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8780 Z= 0.224 Angle : 0.696 10.185 11894 Z= 0.360 Chirality : 0.045 0.184 1352 Planarity : 0.004 0.040 1501 Dihedral : 5.756 53.374 1194 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.96 % Allowed : 25.13 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.26), residues: 1078 helix: 1.56 (0.28), residues: 352 sheet: -0.31 (0.34), residues: 239 loop : -2.25 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP B 169 HIS 0.004 0.001 HIS B 311 PHE 0.042 0.001 PHE B 235 TYR 0.007 0.001 TYR H 178 ARG 0.002 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 1.031 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 20 GLU cc_start: 0.9030 (tp30) cc_final: 0.8606 (tp30) REVERT: A 39 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7895 (tt) REVERT: A 270 ASN cc_start: 0.8611 (t0) cc_final: 0.8367 (t0) REVERT: A 291 TYR cc_start: 0.7334 (t80) cc_final: 0.6895 (t80) REVERT: A 313 ARG cc_start: 0.8915 (mmt90) cc_final: 0.8701 (mmm160) REVERT: A 323 MET cc_start: 0.8597 (ptm) cc_final: 0.8285 (ptm) REVERT: A 349 ARG cc_start: 0.8614 (tpp80) cc_final: 0.8056 (ttm110) REVERT: B 59 TYR cc_start: 0.8767 (m-80) cc_final: 0.8490 (m-80) REVERT: B 175 GLN cc_start: 0.8548 (pm20) cc_final: 0.7805 (pm20) REVERT: B 259 GLN cc_start: 0.7398 (mm-40) cc_final: 0.6727 (mm110) REVERT: G 27 ARG cc_start: 0.7024 (ptt-90) cc_final: 0.6238 (ptt90) REVERT: G 46 LYS cc_start: 0.8888 (tptp) cc_final: 0.8487 (tppt) REVERT: H 141 GLU cc_start: 0.8375 (tp30) cc_final: 0.8060 (tp30) REVERT: R 106 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8955 (mm) REVERT: R 155 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8675 (tp30) REVERT: R 166 LYS cc_start: 0.7984 (mttm) cc_final: 0.7766 (mmtt) REVERT: R 206 ASN cc_start: 0.8263 (t0) cc_final: 0.7984 (t0) REVERT: R 207 ASP cc_start: 0.8522 (p0) cc_final: 0.8188 (t0) REVERT: R 416 CYS cc_start: 0.7882 (t) cc_final: 0.7121 (p) REVERT: R 445 ASN cc_start: 0.8106 (t0) cc_final: 0.7855 (t0) outliers start: 37 outliers final: 31 residues processed: 214 average time/residue: 0.1922 time to fit residues: 57.7158 Evaluate side-chains 215 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 402 TRP Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 442 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.122406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.096863 restraints weight = 18350.937| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.66 r_work: 0.3285 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8780 Z= 0.202 Angle : 0.713 17.752 11894 Z= 0.362 Chirality : 0.045 0.188 1352 Planarity : 0.004 0.040 1501 Dihedral : 5.481 44.167 1194 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.85 % Allowed : 25.13 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.26), residues: 1078 helix: 1.62 (0.28), residues: 352 sheet: -0.35 (0.34), residues: 241 loop : -2.24 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 169 HIS 0.006 0.001 HIS B 311 PHE 0.043 0.001 PHE B 235 TYR 0.007 0.001 TYR R 231 ARG 0.002 0.000 ARG A 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.971 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.9028 (tp30) cc_final: 0.8609 (tp30) REVERT: A 39 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7841 (tt) REVERT: A 270 ASN cc_start: 0.8629 (t0) cc_final: 0.8391 (t0) REVERT: A 291 TYR cc_start: 0.7372 (t80) cc_final: 0.6866 (t80) REVERT: A 313 ARG cc_start: 0.8915 (mmt90) cc_final: 0.8696 (mmm160) REVERT: A 323 MET cc_start: 0.8597 (ptm) cc_final: 0.8276 (ptm) REVERT: A 349 ARG cc_start: 0.8604 (tpp80) cc_final: 0.8052 (ttm110) REVERT: B 59 TYR cc_start: 0.8759 (m-80) cc_final: 0.8536 (m-80) REVERT: B 175 GLN cc_start: 0.8473 (pm20) cc_final: 0.7777 (pm20) REVERT: B 259 GLN cc_start: 0.7374 (mm-40) cc_final: 0.6705 (mm110) REVERT: B 262 MET cc_start: 0.9105 (mmm) cc_final: 0.8814 (mmm) REVERT: G 27 ARG cc_start: 0.7043 (ptt-90) cc_final: 0.6327 (ptt90) REVERT: G 46 LYS cc_start: 0.8899 (tptp) cc_final: 0.8506 (tppt) REVERT: H 141 GLU cc_start: 0.8389 (tp30) cc_final: 0.8086 (tp30) REVERT: H 219 GLN cc_start: 0.8391 (pp30) cc_final: 0.7639 (pp30) REVERT: R 106 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8913 (mm) REVERT: R 155 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8682 (tp30) REVERT: R 206 ASN cc_start: 0.8275 (t0) cc_final: 0.8011 (t0) REVERT: R 207 ASP cc_start: 0.8515 (p0) cc_final: 0.8194 (t0) REVERT: R 435 SER cc_start: 0.9249 (t) cc_final: 0.8687 (p) REVERT: R 445 ASN cc_start: 0.8045 (t0) cc_final: 0.7790 (t0) outliers start: 36 outliers final: 30 residues processed: 212 average time/residue: 0.1895 time to fit residues: 56.6862 Evaluate side-chains 214 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 399 VAL Chi-restraints excluded: chain R residue 402 TRP Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 442 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 0.3980 chunk 14 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 0.0170 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.124803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099402 restraints weight = 18235.872| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.65 r_work: 0.3320 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8780 Z= 0.178 Angle : 0.698 14.231 11894 Z= 0.352 Chirality : 0.044 0.188 1352 Planarity : 0.003 0.040 1501 Dihedral : 4.958 26.166 1194 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.67 % Allowed : 26.52 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.26), residues: 1078 helix: 1.65 (0.28), residues: 353 sheet: -0.20 (0.35), residues: 232 loop : -2.18 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 47 HIS 0.005 0.001 HIS B 311 PHE 0.041 0.001 PHE B 235 TYR 0.008 0.001 TYR R 231 ARG 0.002 0.000 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4531.69 seconds wall clock time: 78 minutes 37.48 seconds (4717.48 seconds total)