Starting phenix.real_space_refine on Fri Nov 15 00:06:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u02_41776/11_2024/8u02_41776.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u02_41776/11_2024/8u02_41776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u02_41776/11_2024/8u02_41776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u02_41776/11_2024/8u02_41776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u02_41776/11_2024/8u02_41776.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u02_41776/11_2024/8u02_41776.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 4956 2.51 5 N 1299 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7774 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2136 Classifications: {'peptide': 272} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2657 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 336} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2544 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 426 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.41, per 1000 atoms: 0.70 Number of scatterers: 7774 At special positions: 0 Unit cell: (83.904, 101.384, 130.226, 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 1460 8.00 N 1299 7.00 C 4956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 182 " distance=2.03 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: 1.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 50.9% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'R' and resid 37 through 40 Processing helix chain 'R' and resid 41 through 61 Processing helix chain 'R' and resid 67 through 87 Processing helix chain 'R' and resid 87 through 97 Processing helix chain 'R' and resid 103 through 138 Processing helix chain 'R' and resid 138 through 143 removed outlier: 3.503A pdb=" N TYR R 142 " --> pdb=" O MET R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 168 Processing helix chain 'R' and resid 169 through 172 removed outlier: 3.600A pdb=" N PHE R 172 " --> pdb=" O PRO R 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 169 through 172' Processing helix chain 'R' and resid 186 through 198 removed outlier: 4.166A pdb=" N TYR R 192 " --> pdb=" O ALA R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 224 removed outlier: 3.555A pdb=" N ARG R 222 " --> pdb=" O ARG R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 399 removed outlier: 4.356A pdb=" N ALA R 376 " --> pdb=" O THR R 372 " (cutoff:3.500A) Proline residue: R 388 - end of helix removed outlier: 4.208A pdb=" N ILE R 397 " --> pdb=" O HIS R 393 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 428 removed outlier: 3.521A pdb=" N TYR R 416 " --> pdb=" O THR R 412 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 430 through 441 Processing helix chain 'B' and resid 7 through 32 removed outlier: 4.006A pdb=" N LYS B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 69 through 92 Processing helix chain 'B' and resid 98 through 113 removed outlier: 4.208A pdb=" N ALA B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 103 " --> pdb=" O GLU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 134 through 143 removed outlier: 3.697A pdb=" N GLN B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 159 Processing helix chain 'B' and resid 159 through 166 Processing helix chain 'B' and resid 208 through 214 removed outlier: 3.731A pdb=" N TRP B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 229 through 233 removed outlier: 4.028A pdb=" N ASP B 232 " --> pdb=" O SER B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 242 through 256 Processing helix chain 'B' and resid 271 through 279 Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 331 through 352 Processing helix chain 'A' and resid 3 through 24 Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.742A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 192 removed outlier: 6.518A pdb=" N VAL B 34 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE B 200 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU B 36 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS B 35 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE B 223 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU B 37 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N CYS B 225 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B 39 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N ALA B 227 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 51 removed outlier: 6.902A pdb=" N ILE A 338 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N THR A 50 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 336 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 63 removed outlier: 3.913A pdb=" N SER A 74 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 79 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA A 92 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 81 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 105 removed outlier: 6.991A pdb=" N GLY A 115 " --> pdb=" O MET A 101 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS A 103 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA A 113 " --> pdb=" O CYS A 103 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR A 105 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR A 111 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N CYS A 121 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU A 138 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 123 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG A 134 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 153 removed outlier: 3.727A pdb=" N CYS A 148 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLN A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASP A 170 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN A 176 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 187 through 192 removed outlier: 3.698A pdb=" N SER A 189 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP A 212 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N CYS A 218 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 229 through 234 removed outlier: 3.527A pdb=" N ALA A 231 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS A 250 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR A 263 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 252 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 273 through 278 removed outlier: 3.848A pdb=" N SER A 275 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS A 294 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL A 307 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 296 " --> pdb=" O ALA A 305 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1281 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: 2.28 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2510 1.34 - 1.46: 1767 1.46 - 1.58: 3559 1.58 - 1.70: 0 1.70 - 1.83: 85 Bond restraints: 7921 Sorted by residual: bond pdb=" N ILE B 213 " pdb=" CA ILE B 213 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N ILE B 286 " pdb=" CA ILE B 286 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.22e+00 bond pdb=" N TRP B 212 " pdb=" CA TRP B 212 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.35e-02 5.49e+03 8.05e+00 bond pdb=" N THR R 205 " pdb=" CA THR R 205 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.41e+00 bond pdb=" N CYS B 287 " pdb=" CA CYS B 287 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.28e-02 6.10e+03 7.34e+00 ... (remaining 7916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 9806 1.63 - 3.26: 805 3.26 - 4.89: 126 4.89 - 6.52: 19 6.52 - 8.15: 8 Bond angle restraints: 10764 Sorted by residual: angle pdb=" N GLU B 43 " pdb=" CA GLU B 43 " pdb=" C GLU B 43 " ideal model delta sigma weight residual 111.69 103.54 8.15 1.23e+00 6.61e-01 4.40e+01 angle pdb=" N ARG B 179 " pdb=" CA ARG B 179 " pdb=" C ARG B 179 " ideal model delta sigma weight residual 112.24 105.31 6.93 1.28e+00 6.10e-01 2.93e+01 angle pdb=" N ILE R 212 " pdb=" CA ILE R 212 " pdb=" C ILE R 212 " ideal model delta sigma weight residual 110.62 105.51 5.11 1.02e+00 9.61e-01 2.51e+01 angle pdb=" CA LEU B 353 " pdb=" C LEU B 353 " pdb=" O LEU B 353 " ideal model delta sigma weight residual 121.16 115.77 5.39 1.12e+00 7.97e-01 2.32e+01 angle pdb=" N LEU B 353 " pdb=" CA LEU B 353 " pdb=" C LEU B 353 " ideal model delta sigma weight residual 110.28 103.22 7.06 1.48e+00 4.57e-01 2.27e+01 ... (remaining 10759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 4531 16.95 - 33.89: 124 33.89 - 50.84: 40 50.84 - 67.78: 9 67.78 - 84.73: 6 Dihedral angle restraints: 4710 sinusoidal: 1746 harmonic: 2964 Sorted by residual: dihedral pdb=" CD ARG B 209 " pdb=" NE ARG B 209 " pdb=" CZ ARG B 209 " pdb=" NH1 ARG B 209 " ideal model delta sinusoidal sigma weight residual 0.00 -84.73 84.73 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CD ARG A 129 " pdb=" NE ARG A 129 " pdb=" CZ ARG A 129 " pdb=" NH1 ARG A 129 " ideal model delta sinusoidal sigma weight residual 0.00 40.13 -40.13 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" C ASP A 205 " pdb=" N ASP A 205 " pdb=" CA ASP A 205 " pdb=" CB ASP A 205 " ideal model delta harmonic sigma weight residual -122.60 -113.37 -9.23 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 4707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 931 0.055 - 0.110: 257 0.110 - 0.165: 65 0.165 - 0.220: 14 0.220 - 0.274: 2 Chirality restraints: 1269 Sorted by residual: chirality pdb=" CA ASP A 205 " pdb=" N ASP A 205 " pdb=" C ASP A 205 " pdb=" CB ASP A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA LEU B 353 " pdb=" N LEU B 353 " pdb=" C LEU B 353 " pdb=" CB LEU B 353 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ILE R 212 " pdb=" N ILE R 212 " pdb=" C ILE R 212 " pdb=" CB ILE R 212 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1266 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 209 " -0.967 9.50e-02 1.11e+02 4.34e-01 1.22e+02 pdb=" NE ARG B 209 " 0.077 2.00e-02 2.50e+03 pdb=" CZ ARG B 209 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG B 209 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 209 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 129 " -0.704 9.50e-02 1.11e+02 3.16e-01 6.07e+01 pdb=" NE ARG A 129 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG A 129 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 129 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 129 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 382 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C PHE R 382 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE R 382 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE R 383 " 0.024 2.00e-02 2.50e+03 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1281 2.76 - 3.29: 8013 3.29 - 3.83: 13215 3.83 - 4.36: 16249 4.36 - 4.90: 26749 Nonbonded interactions: 65507 Sorted by model distance: nonbonded pdb=" O PRO R 423 " pdb=" OG1 THR R 427 " model vdw 2.222 3.040 nonbonded pdb=" OG SER B 126 " pdb=" NH1 ARG B 130 " model vdw 2.258 3.120 nonbonded pdb=" CD1 LEU R 216 " pdb=" OH TYR B 354 " model vdw 2.274 3.460 nonbonded pdb=" O CYS B 255 " pdb=" NZ LYS B 317 " model vdw 2.278 3.120 nonbonded pdb=" OE1 GLU B 217 " pdb=" NZ LYS A 57 " model vdw 2.279 3.120 ... (remaining 65502 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.320 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 0.005 0.041 7921 Z= 0.332 Angle : 0.977 8.155 10764 Z= 0.649 Chirality : 0.056 0.274 1269 Planarity : 0.016 0.434 1360 Dihedral : 10.236 84.730 2785 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.61 % Allowed : 1.33 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.65 (0.25), residues: 1001 helix: 0.46 (0.21), residues: 465 sheet: 1.39 (0.38), residues: 172 loop : 0.13 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 63 HIS 0.010 0.002 HIS R 393 PHE 0.027 0.003 PHE A 234 TYR 0.040 0.003 TYR B 69 ARG 0.049 0.002 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 267 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 218 ASP cc_start: 0.8420 (p0) cc_final: 0.8028 (p0) REVERT: B 263 THR cc_start: 0.8988 (m) cc_final: 0.8754 (p) REVERT: B 307 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8298 (mm110) REVERT: A 14 LEU cc_start: 0.9348 (mt) cc_final: 0.9041 (mt) REVERT: A 59 TYR cc_start: 0.8269 (m-80) cc_final: 0.8019 (m-80) outliers start: 5 outliers final: 1 residues processed: 270 average time/residue: 0.2350 time to fit residues: 81.5806 Evaluate side-chains 163 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 208 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 0.0470 chunk 41 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 418 ASN B 173 GLN B 196 HIS B 214 HIS A 62 HIS A 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 7921 Z= 0.234 Angle : 0.673 8.756 10764 Z= 0.356 Chirality : 0.044 0.209 1269 Planarity : 0.004 0.038 1360 Dihedral : 4.582 44.257 1086 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.18 % Allowed : 11.77 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.26), residues: 1001 helix: 1.57 (0.23), residues: 479 sheet: 1.18 (0.37), residues: 180 loop : 0.09 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 169 HIS 0.005 0.001 HIS R 393 PHE 0.029 0.002 PHE A 241 TYR 0.027 0.002 TYR B 69 ARG 0.006 0.001 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 95 GLU cc_start: 0.8628 (tp30) cc_final: 0.8417 (tp30) REVERT: R 394 ILE cc_start: 0.8845 (pt) cc_final: 0.8525 (mm) REVERT: A 217 MET cc_start: 0.8567 (ppp) cc_final: 0.8327 (ppp) REVERT: A 228 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7756 (m-30) outliers start: 18 outliers final: 7 residues processed: 183 average time/residue: 0.1946 time to fit residues: 48.5617 Evaluate side-chains 148 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 294 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7921 Z= 0.186 Angle : 0.619 11.581 10764 Z= 0.324 Chirality : 0.043 0.150 1269 Planarity : 0.004 0.045 1360 Dihedral : 4.357 39.892 1085 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.94 % Allowed : 13.23 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.27), residues: 1001 helix: 1.72 (0.23), residues: 479 sheet: 1.18 (0.38), residues: 181 loop : -0.09 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 90 HIS 0.011 0.001 HIS B 322 PHE 0.024 0.002 PHE A 241 TYR 0.021 0.001 TYR B 69 ARG 0.004 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 149 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8626 (mmmm) REVERT: R 369 LYS cc_start: 0.8920 (mttt) cc_final: 0.8707 (pptt) REVERT: R 394 ILE cc_start: 0.8839 (pt) cc_final: 0.8619 (mm) REVERT: B 88 MET cc_start: 0.6504 (mmm) cc_final: 0.6179 (tpt) REVERT: B 308 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7938 (m-10) REVERT: A 13 GLN cc_start: 0.8995 (pp30) cc_final: 0.8606 (pp30) REVERT: A 217 MET cc_start: 0.8608 (ppp) cc_final: 0.8327 (ppp) outliers start: 16 outliers final: 8 residues processed: 175 average time/residue: 0.2044 time to fit residues: 48.5941 Evaluate side-chains 151 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 294 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS A 75 GLN A 268 ASN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7921 Z= 0.274 Angle : 0.640 11.033 10764 Z= 0.334 Chirality : 0.044 0.189 1269 Planarity : 0.004 0.048 1360 Dihedral : 4.514 46.507 1085 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.55 % Allowed : 13.71 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.27), residues: 1001 helix: 1.77 (0.24), residues: 481 sheet: 1.11 (0.37), residues: 183 loop : -0.19 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 90 HIS 0.005 0.001 HIS B 322 PHE 0.023 0.002 PHE A 241 TYR 0.022 0.001 TYR A 85 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 174 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7181 (pp) REVERT: R 367 LYS cc_start: 0.9216 (mmtp) cc_final: 0.8998 (mmmt) REVERT: R 369 LYS cc_start: 0.8985 (mttt) cc_final: 0.8742 (pptt) REVERT: B 88 MET cc_start: 0.6389 (mmm) cc_final: 0.5797 (tpt) REVERT: A 61 MET cc_start: 0.8683 (tmm) cc_final: 0.8327 (tmm) REVERT: A 301 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8261 (mmtt) REVERT: A 317 CYS cc_start: 0.7866 (m) cc_final: 0.7502 (p) outliers start: 21 outliers final: 15 residues processed: 165 average time/residue: 0.1968 time to fit residues: 44.4392 Evaluate side-chains 149 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 421 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS A 17 GLN A 75 GLN A 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7921 Z= 0.199 Angle : 0.609 10.716 10764 Z= 0.310 Chirality : 0.042 0.149 1269 Planarity : 0.003 0.046 1360 Dihedral : 4.368 46.178 1085 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.16 % Allowed : 14.32 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.27), residues: 1001 helix: 1.78 (0.24), residues: 481 sheet: 0.84 (0.36), residues: 190 loop : -0.36 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 90 HIS 0.004 0.001 HIS R 393 PHE 0.021 0.002 PHE A 241 TYR 0.017 0.001 TYR B 69 ARG 0.006 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 48 ILE cc_start: 0.9474 (mt) cc_final: 0.9199 (tp) REVERT: R 149 LYS cc_start: 0.8868 (mmtt) cc_final: 0.8585 (mmmm) REVERT: R 174 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7218 (pp) REVERT: B 88 MET cc_start: 0.6428 (mmm) cc_final: 0.6084 (tpt) REVERT: A 61 MET cc_start: 0.8646 (tmm) cc_final: 0.8228 (tmm) REVERT: A 317 CYS cc_start: 0.7917 (m) cc_final: 0.7560 (p) REVERT: C 38 MET cc_start: 0.8688 (ptp) cc_final: 0.8325 (ptp) REVERT: C 48 ASP cc_start: 0.8372 (t70) cc_final: 0.7621 (t0) outliers start: 26 outliers final: 15 residues processed: 168 average time/residue: 0.2037 time to fit residues: 46.6718 Evaluate side-chains 153 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 70 ASN B 196 HIS A 75 GLN C 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7921 Z= 0.200 Angle : 0.622 11.047 10764 Z= 0.314 Chirality : 0.043 0.157 1269 Planarity : 0.003 0.047 1360 Dihedral : 4.333 44.223 1085 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.16 % Allowed : 16.02 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.27), residues: 1001 helix: 1.83 (0.24), residues: 480 sheet: 0.77 (0.36), residues: 190 loop : -0.44 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 90 HIS 0.004 0.001 HIS R 393 PHE 0.020 0.001 PHE A 241 TYR 0.027 0.001 TYR B 69 ARG 0.005 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 80 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8641 (t0) REVERT: R 82 LEU cc_start: 0.9172 (mt) cc_final: 0.8887 (mp) REVERT: R 174 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7415 (pp) REVERT: B 88 MET cc_start: 0.6178 (mmm) cc_final: 0.5565 (tpt) REVERT: B 278 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8350 (ttmt) REVERT: B 322 HIS cc_start: 0.8296 (t-90) cc_final: 0.8057 (t-90) REVERT: A 61 MET cc_start: 0.8624 (tmm) cc_final: 0.8189 (tmm) REVERT: A 317 CYS cc_start: 0.7939 (m) cc_final: 0.7569 (p) REVERT: C 38 MET cc_start: 0.8654 (ptp) cc_final: 0.8335 (ptp) REVERT: C 48 ASP cc_start: 0.8406 (t70) cc_final: 0.7538 (t0) outliers start: 26 outliers final: 17 residues processed: 165 average time/residue: 0.2168 time to fit residues: 47.1795 Evaluate side-chains 160 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 417 VAL Chi-restraints excluded: chain R residue 421 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS A 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7921 Z= 0.200 Angle : 0.634 13.399 10764 Z= 0.314 Chirality : 0.043 0.143 1269 Planarity : 0.004 0.047 1360 Dihedral : 4.312 46.875 1085 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.91 % Allowed : 17.11 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.27), residues: 1001 helix: 1.85 (0.24), residues: 481 sheet: 0.71 (0.36), residues: 181 loop : -0.46 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 90 HIS 0.004 0.001 HIS R 393 PHE 0.019 0.001 PHE A 241 TYR 0.022 0.001 TYR B 69 ARG 0.004 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 48 ILE cc_start: 0.9424 (mt) cc_final: 0.9221 (tp) REVERT: R 62 GLU cc_start: 0.7903 (mp0) cc_final: 0.7617 (mp0) REVERT: R 71 TYR cc_start: 0.8007 (m-80) cc_final: 0.7577 (m-80) REVERT: R 82 LEU cc_start: 0.9173 (mt) cc_final: 0.8889 (mp) REVERT: B 88 MET cc_start: 0.6306 (mmm) cc_final: 0.5657 (tpt) REVERT: B 278 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8363 (ttmt) REVERT: A 61 MET cc_start: 0.8620 (tmm) cc_final: 0.8234 (tmm) REVERT: A 127 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8493 (mmmm) REVERT: A 317 CYS cc_start: 0.7947 (m) cc_final: 0.7588 (p) REVERT: C 38 MET cc_start: 0.8621 (ptp) cc_final: 0.8281 (ptp) REVERT: C 48 ASP cc_start: 0.8404 (t70) cc_final: 0.7775 (t0) outliers start: 24 outliers final: 19 residues processed: 165 average time/residue: 0.2134 time to fit residues: 46.7172 Evaluate side-chains 159 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 385 CYS Chi-restraints excluded: chain R residue 418 ASN Chi-restraints excluded: chain R residue 421 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7921 Z= 0.230 Angle : 0.645 11.531 10764 Z= 0.322 Chirality : 0.043 0.149 1269 Planarity : 0.004 0.073 1360 Dihedral : 4.389 48.618 1085 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.03 % Allowed : 17.60 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.27), residues: 1001 helix: 1.77 (0.24), residues: 482 sheet: 0.65 (0.36), residues: 185 loop : -0.52 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 90 HIS 0.004 0.001 HIS R 393 PHE 0.018 0.002 PHE A 241 TYR 0.021 0.001 TYR B 69 ARG 0.004 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 62 GLU cc_start: 0.7935 (mp0) cc_final: 0.7637 (mp0) REVERT: B 88 MET cc_start: 0.6358 (mmm) cc_final: 0.5647 (tpt) REVERT: B 128 MET cc_start: 0.8300 (mmm) cc_final: 0.8053 (mmm) REVERT: B 129 MET cc_start: 0.7498 (mmt) cc_final: 0.7263 (mtt) REVERT: B 278 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8306 (ttmt) REVERT: B 323 MET cc_start: 0.8029 (mmm) cc_final: 0.7677 (mmm) REVERT: A 61 MET cc_start: 0.8639 (tmm) cc_final: 0.8237 (tmm) REVERT: A 317 CYS cc_start: 0.7949 (m) cc_final: 0.7638 (p) REVERT: C 31 SER cc_start: 0.9239 (p) cc_final: 0.9019 (m) REVERT: C 48 ASP cc_start: 0.8438 (t70) cc_final: 0.7669 (t0) outliers start: 25 outliers final: 22 residues processed: 156 average time/residue: 0.2253 time to fit residues: 46.8801 Evaluate side-chains 164 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 385 CYS Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 417 VAL Chi-restraints excluded: chain R residue 418 ASN Chi-restraints excluded: chain R residue 421 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7921 Z= 0.280 Angle : 0.682 11.708 10764 Z= 0.343 Chirality : 0.043 0.155 1269 Planarity : 0.004 0.058 1360 Dihedral : 4.559 54.761 1085 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.16 % Allowed : 17.84 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.27), residues: 1001 helix: 1.74 (0.24), residues: 482 sheet: 0.50 (0.36), residues: 185 loop : -0.52 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP R 90 HIS 0.004 0.001 HIS R 393 PHE 0.018 0.002 PHE A 241 TYR 0.020 0.001 TYR B 69 ARG 0.004 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 62 GLU cc_start: 0.7935 (mp0) cc_final: 0.7584 (mp0) REVERT: B 128 MET cc_start: 0.8254 (mmm) cc_final: 0.8001 (mmm) REVERT: B 129 MET cc_start: 0.7575 (mmt) cc_final: 0.7168 (mtt) REVERT: B 323 MET cc_start: 0.8071 (mmm) cc_final: 0.7726 (mmm) REVERT: A 317 CYS cc_start: 0.7954 (m) cc_final: 0.7721 (p) REVERT: C 31 SER cc_start: 0.9255 (p) cc_final: 0.9036 (m) REVERT: C 48 ASP cc_start: 0.8481 (t70) cc_final: 0.8017 (t70) outliers start: 26 outliers final: 24 residues processed: 157 average time/residue: 0.2260 time to fit residues: 46.7198 Evaluate side-chains 160 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 385 CYS Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 417 VAL Chi-restraints excluded: chain R residue 418 ASN Chi-restraints excluded: chain R residue 421 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 78 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS B 205 GLN A 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7921 Z= 0.209 Angle : 0.707 12.069 10764 Z= 0.347 Chirality : 0.044 0.185 1269 Planarity : 0.004 0.047 1360 Dihedral : 4.453 53.845 1085 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.91 % Allowed : 18.93 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.27), residues: 1001 helix: 1.78 (0.24), residues: 485 sheet: 0.75 (0.37), residues: 176 loop : -0.53 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 90 HIS 0.004 0.001 HIS R 393 PHE 0.018 0.001 PHE A 241 TYR 0.019 0.001 TYR B 69 ARG 0.007 0.001 ARG R 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 62 GLU cc_start: 0.8029 (mp0) cc_final: 0.7749 (mp0) REVERT: R 71 TYR cc_start: 0.7885 (m-80) cc_final: 0.7508 (m-80) REVERT: R 82 LEU cc_start: 0.9142 (mt) cc_final: 0.8913 (mp) REVERT: R 149 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8534 (mmmm) REVERT: B 307 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7865 (tp-100) REVERT: B 323 MET cc_start: 0.8037 (mmm) cc_final: 0.7698 (mmm) REVERT: A 61 MET cc_start: 0.8658 (tmm) cc_final: 0.8436 (tmm) REVERT: A 280 LYS cc_start: 0.8983 (tmtt) cc_final: 0.8591 (tmmt) REVERT: A 317 CYS cc_start: 0.7925 (m) cc_final: 0.7609 (p) REVERT: C 31 SER cc_start: 0.9237 (p) cc_final: 0.9025 (m) REVERT: C 48 ASP cc_start: 0.8393 (t70) cc_final: 0.7982 (t70) outliers start: 24 outliers final: 22 residues processed: 155 average time/residue: 0.2040 time to fit residues: 42.4192 Evaluate side-chains 159 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 385 CYS Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 417 VAL Chi-restraints excluded: chain R residue 418 ASN Chi-restraints excluded: chain R residue 421 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS A 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.107721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.075075 restraints weight = 19616.130| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 4.17 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7921 Z= 0.212 Angle : 0.712 12.347 10764 Z= 0.351 Chirality : 0.044 0.174 1269 Planarity : 0.004 0.047 1360 Dihedral : 4.443 55.744 1085 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.55 % Allowed : 19.90 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.27), residues: 1001 helix: 1.76 (0.24), residues: 486 sheet: 0.73 (0.37), residues: 172 loop : -0.52 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 90 HIS 0.004 0.001 HIS R 393 PHE 0.017 0.001 PHE A 241 TYR 0.018 0.001 TYR B 69 ARG 0.006 0.000 ARG R 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2072.52 seconds wall clock time: 38 minutes 39.27 seconds (2319.27 seconds total)