Starting phenix.real_space_refine on Sat Dec 28 13:54:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ej0_31147/12_2024/7ej0_31147.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ej0_31147/12_2024/7ej0_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_31147/12_2024/7ej0_31147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ej0_31147/12_2024/7ej0_31147.map" model { file = "/net/cci-nas-00/data/ceres_data/7ej0_31147/12_2024/7ej0_31147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ej0_31147/12_2024/7ej0_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.40, per 1000 atoms: 0.63 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: 2.35 Conformation dependent library (CDL) restraints added in 1.2 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: 0.91 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: 2.42 Time building geometry restraints manager: 2.65 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: 1.010 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: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.090 Find NCS groups from input model: 0.100 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.690 ------------------------------------------------------------------------------- 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 : 0.924 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: 0.2012 time to fit residues: 77.4337 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 : 0.901 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 53.254 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 : 0.957 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: 0.7127 (ppp) cc_final: 0.6423 (pmm) REVERT: A 291 TYR cc_start: 0.7467 (t80) cc_final: 0.6924 (t80) REVERT: A 349 ARG cc_start: 0.7972 (tpp80) cc_final: 0.7543 (ttm110) REVERT: B 169 TRP cc_start: 0.7630 (m-10) cc_final: 0.7335 (m-10) REVERT: B 312 ASP cc_start: 0.6589 (t0) cc_final: 0.6386 (t0) REVERT: G 27 ARG cc_start: 0.6755 (ptt-90) cc_final: 0.6298 (ptt90) REVERT: G 46 LYS cc_start: 0.8850 (tptp) cc_final: 0.8473 (tppt) REVERT: H 68 PHE cc_start: 0.7827 (m-10) cc_final: 0.7597 (m-10) REVERT: R 155 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8408 (tp30) REVERT: R 206 ASN cc_start: 0.8190 (t0) cc_final: 0.7912 (t0) REVERT: R 207 ASP cc_start: 0.8577 (p0) cc_final: 0.7943 (t0) REVERT: R 236 GLN cc_start: 0.8644 (mm110) cc_final: 0.8237 (mt0) REVERT: R 445 ASN cc_start: 0.8080 (t0) cc_final: 0.7801 (t0) outliers start: 20 outliers final: 12 residues processed: 224 average time/residue: 0.1975 time to fit residues: 61.6127 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 : 1.045 ------------------------------------------------------------------------------- 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 54 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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** B 13 GLN B 293 ASN R 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8780 Z= 0.280 Angle : 0.700 9.805 11894 Z= 0.367 Chirality : 0.046 0.177 1352 Planarity : 0.004 0.056 1501 Dihedral : 5.673 51.457 1196 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.53 % Allowed : 17.86 % Favored : 78.61 % 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: -0.78 (0.25), residues: 1078 helix: 1.21 (0.29), residues: 347 sheet: -0.20 (0.32), residues: 248 loop : -2.03 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 47 HIS 0.010 0.001 HIS B 311 PHE 0.019 0.002 PHE B 241 TYR 0.010 0.001 TYR R 231 ARG 0.004 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 236 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.973 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: 0.7184 (ppp) cc_final: 0.6492 (pmm) REVERT: A 349 ARG cc_start: 0.8148 (tpp80) cc_final: 0.7679 (ttm110) REVERT: B 175 GLN cc_start: 0.8211 (pm20) cc_final: 0.7639 (pm20) REVERT: B 259 GLN cc_start: 0.6871 (mm-40) cc_final: 0.6304 (mm110) REVERT: B 312 ASP cc_start: 0.6844 (t0) cc_final: 0.6638 (t0) REVERT: G 27 ARG cc_start: 0.6899 (ptt-90) cc_final: 0.6444 (ptt90) REVERT: G 46 LYS cc_start: 0.8779 (tptp) cc_final: 0.8407 (tppt) REVERT: H 141 GLU cc_start: 0.8257 (tp30) cc_final: 0.7904 (tp30) REVERT: R 155 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8385 (tp30) REVERT: R 206 ASN cc_start: 0.8162 (t0) cc_final: 0.7856 (t0) REVERT: R 207 ASP cc_start: 0.8508 (p0) cc_final: 0.7971 (t0) REVERT: R 236 GLN cc_start: 0.8578 (mm110) cc_final: 0.8270 (mt0) REVERT: R 445 ASN cc_start: 0.7979 (t0) cc_final: 0.7709 (t0) outliers start: 33 outliers final: 22 residues processed: 226 average time/residue: 0.2021 time to fit residues: 63.3297 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 : 1.060 ------------------------------------------------------------------------------- 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 399 VAL Chi-restraints excluded: chain R residue 400 VAL Chi-restraints excluded: chain R residue 411 LEU 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 97 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 293 ASN H 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8780 Z= 0.226 Angle : 0.667 10.016 11894 Z= 0.350 Chirality : 0.045 0.170 1352 Planarity : 0.004 0.044 1501 Dihedral : 5.437 45.337 1196 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.10 % Allowed : 20.21 % Favored : 76.68 % 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: -0.73 (0.25), residues: 1078 helix: 1.37 (0.29), residues: 347 sheet: -0.24 (0.33), residues: 248 loop : -2.07 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.007 0.001 HIS B 311 PHE 0.021 0.001 PHE B 241 TYR 0.007 0.001 TYR H 178 ARG 0.005 0.000 ARG A 206 *********************** 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 220 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 1.024 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: 0.7259 (ppp) cc_final: 0.6584 (pmm) REVERT: A 307 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: A 349 ARG cc_start: 0.8078 (tpp80) cc_final: 0.7599 (ttm110) REVERT: B 312 ASP cc_start: 0.7010 (t0) cc_final: 0.6802 (t0) REVERT: G 27 ARG cc_start: 0.7071 (ptt-90) cc_final: 0.6138 (ptt90) REVERT: G 46 LYS cc_start: 0.8762 (tptp) cc_final: 0.8397 (tppt) REVERT: H 141 GLU cc_start: 0.8248 (tp30) cc_final: 0.7916 (tp30) REVERT: R 106 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8999 (mm) REVERT: R 155 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8392 (tp30) REVERT: R 206 ASN cc_start: 0.8141 (t0) cc_final: 0.7824 (t0) REVERT: R 207 ASP cc_start: 0.8468 (p0) cc_final: 0.7972 (t0) REVERT: R 224 CYS cc_start: 0.8725 (t) cc_final: 0.8384 (t) REVERT: R 236 GLN cc_start: 0.8535 (mm110) cc_final: 0.8309 (mt0) REVERT: R 435 SER cc_start: 0.9207 (t) cc_final: 0.8642 (p) REVERT: R 445 ASN cc_start: 0.7979 (t0) cc_final: 0.7683 (t0) outliers start: 29 outliers final: 19 residues processed: 210 average time/residue: 0.2011 time to fit residues: 58.9147 Evaluate side-chains 199 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 192 LEU 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 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 138 HIS 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 399 VAL Chi-restraints excluded: chain R residue 400 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 442 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 H 39 GLN R 83 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8780 Z= 0.212 Angle : 0.657 10.846 11894 Z= 0.344 Chirality : 0.045 0.217 1352 Planarity : 0.004 0.039 1501 Dihedral : 5.209 37.470 1196 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.96 % Allowed : 20.96 % Favored : 75.08 % 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: -0.69 (0.26), residues: 1078 helix: 1.47 (0.29), residues: 349 sheet: -0.26 (0.33), residues: 248 loop : -2.10 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 47 HIS 0.008 0.001 HIS B 311 PHE 0.021 0.001 PHE B 241 TYR 0.007 0.001 TYR H 178 ARG 0.003 0.000 ARG B 304 *********************** 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 229 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.989 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: 0.7297 (ppp) cc_final: 0.6613 (pmm) REVERT: A 349 ARG cc_start: 0.8136 (tpp80) cc_final: 0.7644 (ttm110) REVERT: G 46 LYS cc_start: 0.8791 (tptp) cc_final: 0.8394 (tppt) REVERT: H 141 GLU cc_start: 0.8296 (tp30) cc_final: 0.7917 (tp30) REVERT: R 106 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8995 (mm) REVERT: R 155 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8387 (tp30) REVERT: R 206 ASN cc_start: 0.8115 (t0) cc_final: 0.7806 (t0) REVERT: R 207 ASP cc_start: 0.8373 (p0) cc_final: 0.7946 (t0) REVERT: R 224 CYS cc_start: 0.8776 (t) cc_final: 0.8437 (t) REVERT: R 422 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8716 (pp) REVERT: R 435 SER cc_start: 0.9197 (t) cc_final: 0.8663 (p) REVERT: R 445 ASN cc_start: 0.7926 (t0) cc_final: 0.7617 (t0) REVERT: R 446 HIS cc_start: 0.8462 (p90) cc_final: 0.8156 (p90) outliers start: 37 outliers final: 22 residues processed: 219 average time/residue: 0.1957 time to fit residues: 60.0728 Evaluate side-chains 207 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 58 ILE 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 316 SER Chi-restraints excluded: chain H residue 2 VAL 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 H residue 222 GLU Chi-restraints excluded: chain R residue 83 GLN 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 391 LEU 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 Chi-restraints excluded: chain R residue 422 LEU 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 35 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 0.2980 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3211 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= 0.280 Angle : 0.686 11.105 11894 Z= 0.360 Chirality : 0.046 0.228 1352 Planarity : 0.004 0.039 1501 Dihedral : 5.514 46.147 1196 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.17 % Allowed : 22.25 % Favored : 73.58 % 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: -0.79 (0.26), residues: 1078 helix: 1.42 (0.29), residues: 349 sheet: -0.33 (0.33), residues: 248 loop : -2.19 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 339 HIS 0.007 0.001 HIS B 311 PHE 0.035 0.002 PHE B 235 TYR 0.010 0.001 TYR H 178 ARG 0.008 0.000 ARG G 27 *********************** 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 221 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.967 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: 0.7283 (ppp) cc_final: 0.6552 (pmm) REVERT: A 349 ARG cc_start: 0.8151 (tpp80) cc_final: 0.7708 (ttm110) REVERT: G 27 ARG cc_start: 0.6884 (ptt-90) cc_final: 0.6374 (ptt90) REVERT: G 28 ILE cc_start: 0.7303 (mt) cc_final: 0.7074 (mm) REVERT: G 42 GLU cc_start: 0.7943 (tp30) cc_final: 0.7405 (tp30) REVERT: G 46 LYS cc_start: 0.8776 (tptp) cc_final: 0.8380 (tppt) REVERT: H 141 GLU cc_start: 0.8302 (tp30) cc_final: 0.7935 (tp30) REVERT: R 106 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9000 (mm) REVERT: R 155 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8418 (tp30) REVERT: R 166 LYS cc_start: 0.7896 (mttm) cc_final: 0.7649 (mmtt) REVERT: R 206 ASN cc_start: 0.8116 (t0) cc_final: 0.7830 (t0) REVERT: R 207 ASP cc_start: 0.8376 (p0) cc_final: 0.7942 (t0) REVERT: R 224 CYS cc_start: 0.8840 (t) cc_final: 0.8548 (t) REVERT: R 233 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.6955 (tpm170) REVERT: R 435 SER cc_start: 0.9220 (t) cc_final: 0.8668 (p) REVERT: R 445 ASN cc_start: 0.7958 (t0) cc_final: 0.7671 (t0) REVERT: R 446 HIS cc_start: 0.8440 (p90) cc_final: 0.8211 (p90) outliers start: 39 outliers final: 28 residues processed: 210 average time/residue: 0.2016 time to fit residues: 58.6373 Evaluate side-chains 208 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 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 316 SER Chi-restraints excluded: chain H residue 2 VAL 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 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 140 CYS Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 391 LEU 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 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 100 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3418 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= 0.276 Angle : 0.692 11.560 11894 Z= 0.363 Chirality : 0.046 0.185 1352 Planarity : 0.004 0.039 1501 Dihedral : 5.646 48.599 1196 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.60 % Allowed : 22.78 % 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: -0.80 (0.26), residues: 1078 helix: 1.47 (0.28), residues: 355 sheet: -0.35 (0.34), residues: 246 loop : -2.27 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 339 HIS 0.006 0.001 HIS B 311 PHE 0.038 0.002 PHE B 235 TYR 0.010 0.001 TYR H 178 ARG 0.004 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 227 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.977 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: 0.8808 (tp30) cc_final: 0.8361 (tp30) REVERT: A 39 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7664 (tt) REVERT: A 270 ASN cc_start: 0.8454 (t0) cc_final: 0.8206 (t0) REVERT: A 291 TYR cc_start: 0.7298 (t80) cc_final: 0.6655 (t80) REVERT: A 349 ARG cc_start: 0.8204 (tpp80) cc_final: 0.7771 (ttm110) REVERT: G 27 ARG cc_start: 0.6968 (ptt-90) cc_final: 0.6320 (ptt90) REVERT: G 28 ILE cc_start: 0.7332 (mt) cc_final: 0.6920 (mm) REVERT: G 42 GLU cc_start: 0.7966 (tp30) cc_final: 0.7429 (tp30) REVERT: G 46 LYS cc_start: 0.8793 (tptp) cc_final: 0.8399 (tppt) REVERT: H 141 GLU cc_start: 0.8365 (tp30) cc_final: 0.8010 (tp30) REVERT: R 106 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8960 (mm) REVERT: R 155 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8400 (tp30) REVERT: R 166 LYS cc_start: 0.7894 (mttm) cc_final: 0.7653 (mmtt) REVERT: R 206 ASN cc_start: 0.8148 (t0) cc_final: 0.7858 (t0) REVERT: R 207 ASP cc_start: 0.8343 (p0) cc_final: 0.8000 (t0) REVERT: R 224 CYS cc_start: 0.8769 (t) cc_final: 0.8500 (t) REVERT: R 416 CYS cc_start: 0.7740 (t) cc_final: 0.6854 (p) REVERT: R 435 SER cc_start: 0.9230 (t) cc_final: 0.8696 (p) REVERT: R 445 ASN cc_start: 0.7982 (t0) cc_final: 0.7705 (t0) outliers start: 43 outliers final: 30 residues processed: 216 average time/residue: 0.1967 time to fit residues: 59.0291 Evaluate side-chains 210 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 139 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 316 SER Chi-restraints excluded: chain H residue 2 VAL 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 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 140 CYS Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 391 LEU 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 Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 440 ILE 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 41 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN R 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3502 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= 0.220 Angle : 0.684 11.109 11894 Z= 0.355 Chirality : 0.045 0.179 1352 Planarity : 0.004 0.040 1501 Dihedral : 5.590 49.585 1194 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.96 % Allowed : 24.39 % Favored : 71.66 % 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: -0.77 (0.26), residues: 1078 helix: 1.49 (0.28), residues: 355 sheet: -0.36 (0.34), residues: 246 loop : -2.23 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 339 HIS 0.004 0.001 HIS B 311 PHE 0.042 0.001 PHE B 235 TYR 0.008 0.001 TYR H 178 ARG 0.004 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 225 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 1.051 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: 0.8820 (tp30) cc_final: 0.8411 (tp30) REVERT: A 39 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7592 (tt) REVERT: A 270 ASN cc_start: 0.8445 (t0) cc_final: 0.8203 (t0) REVERT: A 349 ARG cc_start: 0.8205 (tpp80) cc_final: 0.7614 (ttm110) REVERT: G 27 ARG cc_start: 0.7062 (ptt-90) cc_final: 0.6323 (ptt90) REVERT: G 28 ILE cc_start: 0.7135 (mt) cc_final: 0.6912 (mm) REVERT: G 46 LYS cc_start: 0.8806 (tptp) cc_final: 0.8388 (tppt) REVERT: H 141 GLU cc_start: 0.8345 (tp30) cc_final: 0.7985 (tp30) REVERT: H 208 GLU cc_start: 0.8161 (pp20) cc_final: 0.7936 (pp20) REVERT: R 106 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8914 (mm) REVERT: R 155 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8394 (tp30) REVERT: R 166 LYS cc_start: 0.7902 (mttm) cc_final: 0.7632 (mmtt) REVERT: R 206 ASN cc_start: 0.8108 (t0) cc_final: 0.7816 (t0) REVERT: R 207 ASP cc_start: 0.8315 (p0) cc_final: 0.8022 (t0) REVERT: R 224 CYS cc_start: 0.8763 (t) cc_final: 0.8493 (t) REVERT: R 416 CYS cc_start: 0.7687 (t) cc_final: 0.6801 (p) REVERT: R 435 SER cc_start: 0.9223 (t) cc_final: 0.8690 (p) REVERT: R 445 ASN cc_start: 0.7972 (t0) cc_final: 0.7702 (t0) outliers start: 37 outliers final: 31 residues processed: 214 average time/residue: 0.1972 time to fit residues: 58.6631 Evaluate side-chains 214 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 114 CYS Chi-restraints excluded: chain B residue 139 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 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 134 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain R residue 391 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 42 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 0.0670 chunk 87 optimal weight: 0.0370 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN R 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8780 Z= 0.179 Angle : 0.680 12.834 11894 Z= 0.349 Chirality : 0.044 0.186 1352 Planarity : 0.004 0.040 1501 Dihedral : 5.436 47.493 1194 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.99 % Allowed : 25.03 % Favored : 71.98 % 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: 1.49 (0.28), residues: 348 sheet: -0.31 (0.34), residues: 246 loop : -2.12 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 339 HIS 0.014 0.001 HIS R 138 PHE 0.044 0.001 PHE B 235 TYR 0.007 0.001 TYR R 231 ARG 0.004 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 225 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 1.057 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. REVERT: A 20 GLU cc_start: 0.8775 (tp30) cc_final: 0.8381 (tp30) REVERT: A 39 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7400 (tt) REVERT: A 270 ASN cc_start: 0.8444 (t0) cc_final: 0.8225 (t0) REVERT: A 291 TYR cc_start: 0.7334 (t80) cc_final: 0.6795 (t80) REVERT: A 323 MET cc_start: 0.8184 (ptm) cc_final: 0.7838 (ptm) REVERT: A 349 ARG cc_start: 0.8171 (tpp80) cc_final: 0.7730 (ttm110) REVERT: B 262 MET cc_start: 0.8822 (mmm) cc_final: 0.8571 (mmm) REVERT: G 27 ARG cc_start: 0.7060 (ptt-90) cc_final: 0.6201 (ptt90) REVERT: G 42 GLU cc_start: 0.7876 (tp30) cc_final: 0.7374 (tp30) REVERT: G 46 LYS cc_start: 0.8822 (tptp) cc_final: 0.8420 (tppt) REVERT: H 141 GLU cc_start: 0.8309 (tp30) cc_final: 0.7928 (tp30) REVERT: H 171 GLN cc_start: 0.8579 (mt0) cc_final: 0.8075 (mp10) REVERT: R 155 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8385 (tp30) REVERT: R 206 ASN cc_start: 0.8139 (t0) cc_final: 0.7867 (t0) REVERT: R 207 ASP cc_start: 0.8293 (p0) cc_final: 0.8020 (t0) REVERT: R 224 CYS cc_start: 0.8729 (t) cc_final: 0.8454 (t) REVERT: R 435 SER cc_start: 0.9183 (t) cc_final: 0.8648 (p) REVERT: R 445 ASN cc_start: 0.7915 (t0) cc_final: 0.7646 (t0) outliers start: 28 outliers final: 24 residues processed: 216 average time/residue: 0.1999 time to fit residues: 60.7866 Evaluate side-chains 210 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 114 CYS 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 336 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 62 ASP 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 R residue 96 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 232 VAL Chi-restraints excluded: chain R residue 391 LEU 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 102 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN R 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8780 Z= 0.215 Angle : 0.690 12.098 11894 Z= 0.355 Chirality : 0.045 0.186 1352 Planarity : 0.004 0.034 1501 Dihedral : 5.367 45.354 1194 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.78 % Allowed : 25.45 % Favored : 71.76 % 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: -0.74 (0.26), residues: 1078 helix: 1.52 (0.28), residues: 349 sheet: -0.31 (0.34), residues: 244 loop : -2.18 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 339 HIS 0.007 0.001 HIS R 138 PHE 0.041 0.001 PHE B 235 TYR 0.008 0.001 TYR H 178 ARG 0.004 0.000 ARG A 313 ********************** 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 213 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.979 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: 0.8793 (tp30) cc_final: 0.8372 (tp30) REVERT: A 39 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7527 (tt) REVERT: A 270 ASN cc_start: 0.8444 (t0) cc_final: 0.8213 (t0) REVERT: A 291 TYR cc_start: 0.7252 (t80) cc_final: 0.6699 (t80) REVERT: A 323 MET cc_start: 0.8204 (ptm) cc_final: 0.7863 (ptm) REVERT: A 349 ARG cc_start: 0.8193 (tpp80) cc_final: 0.7648 (ttm110) REVERT: G 27 ARG cc_start: 0.7000 (ptt-90) cc_final: 0.6138 (ptt90) REVERT: G 42 GLU cc_start: 0.7866 (tp30) cc_final: 0.7359 (tp30) REVERT: G 46 LYS cc_start: 0.8833 (tptp) cc_final: 0.8433 (tppt) REVERT: H 141 GLU cc_start: 0.8316 (tp30) cc_final: 0.7956 (tp30) REVERT: H 219 GLN cc_start: 0.8333 (pp30) cc_final: 0.7584 (pp30) REVERT: R 155 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8402 (tp30) REVERT: R 206 ASN cc_start: 0.8165 (t0) cc_final: 0.7865 (t0) REVERT: R 207 ASP cc_start: 0.8292 (p0) cc_final: 0.8020 (t0) REVERT: R 224 CYS cc_start: 0.8776 (t) cc_final: 0.8491 (t) REVERT: R 435 SER cc_start: 0.9213 (t) cc_final: 0.8683 (p) REVERT: R 445 ASN cc_start: 0.7973 (t0) cc_final: 0.7705 (t0) outliers start: 26 outliers final: 22 residues processed: 206 average time/residue: 0.2006 time to fit residues: 57.3191 Evaluate side-chains 207 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 B residue 114 CYS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 237 ASN 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 99 SER Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain R residue 96 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 232 VAL Chi-restraints excluded: chain R residue 391 LEU 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 91 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 0.0070 chunk 15 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN R 138 HIS ** R 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.124847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.099412 restraints weight = 18112.073| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.60 r_work: 0.3324 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3551 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= 0.181 Angle : 0.684 12.161 11894 Z= 0.350 Chirality : 0.044 0.189 1352 Planarity : 0.003 0.034 1501 Dihedral : 5.239 41.606 1194 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.67 % Allowed : 25.56 % Favored : 71.76 % 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: -0.70 (0.26), residues: 1078 helix: 1.53 (0.28), residues: 348 sheet: -0.31 (0.34), residues: 244 loop : -2.13 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 339 HIS 0.008 0.001 HIS R 138 PHE 0.043 0.001 PHE B 235 TYR 0.007 0.001 TYR R 231 ARG 0.004 0.000 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2205.93 seconds wall clock time: 40 minutes 57.01 seconds (2457.01 seconds total)