Starting phenix.real_space_refine on Tue Sep 24 18:33:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbx_23749/09_2024/7mbx_23749.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbx_23749/09_2024/7mbx_23749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbx_23749/09_2024/7mbx_23749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbx_23749/09_2024/7mbx_23749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbx_23749/09_2024/7mbx_23749.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbx_23749/09_2024/7mbx_23749.cif" } resolution = 1.95 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= 0.002 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 63 5.16 5 C 5326 2.51 5 N 1444 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8433 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1959 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2589 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 431 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 976 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 985 Chain: "P" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 77 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2304 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER N 127 " occ=0.50 ... (8 atoms not shown) pdb=" CB BSER N 127 " occ=0.50 Time building chain proxies: 6.09, per 1000 atoms: 0.72 Number of scatterers: 8433 At special positions: 0 Unit cell: (79.4444, 97.7166, 139.028, 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 63 16.00 O 1600 8.00 N 1444 7.00 C 5326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 196 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2014 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 11 sheets defined 44.9% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 11 through 40 removed outlier: 3.733A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.713A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 removed outlier: 3.819A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.152A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.877A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.590A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.589A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.632A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.520A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.734A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 39 through 69 Processing helix chain 'R' and resid 70 through 73 removed outlier: 3.745A pdb=" N ARG R 73 " --> pdb=" O LYS R 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 70 through 73' Processing helix chain 'R' and resid 74 through 105 removed outlier: 3.731A pdb=" N PHE R 79 " --> pdb=" O VAL R 75 " (cutoff:3.500A) Proline residue: R 96 - end of helix Proline residue: R 101 - end of helix Processing helix chain 'R' and resid 110 through 145 Processing helix chain 'R' and resid 145 through 153 removed outlier: 3.851A pdb=" N ARG R 150 " --> pdb=" O PRO R 146 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL R 151 " --> pdb=" O LEU R 147 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TRP R 152 " --> pdb=" O GLN R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 173 removed outlier: 3.617A pdb=" N ALA R 158 " --> pdb=" O THR R 154 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET R 173 " --> pdb=" O SER R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 179 removed outlier: 3.792A pdb=" N ILE R 178 " --> pdb=" O THR R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 218 Processing helix chain 'R' and resid 218 through 243 Processing helix chain 'R' and resid 303 through 339 Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 339 through 348 removed outlier: 3.644A pdb=" N SER R 348 " --> pdb=" O GLU R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 361 Processing helix chain 'R' and resid 361 through 371 Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 374 through 382 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.421A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.719A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.577A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.856A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.501A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.515A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.597A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.693A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.215A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 180 through 186 455 hydrogen bonds defined for protein. 1302 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: 2.61 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1352 1.31 - 1.44: 2328 1.44 - 1.56: 4766 1.56 - 1.69: 5 1.69 - 1.82: 92 Bond restraints: 8543 Sorted by residual: bond pdb=" C LEU A 291 " pdb=" O LEU A 291 " ideal model delta sigma weight residual 1.233 1.179 0.054 1.28e-02 6.10e+03 1.77e+01 bond pdb=" CAI Y01 R 501 " pdb=" CAK Y01 R 501 " ideal model delta sigma weight residual 1.492 1.573 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" CAY Y01 R 501 " pdb=" OAW Y01 R 501 " ideal model delta sigma weight residual 1.332 1.404 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" CA SER A 366 " pdb=" CB SER A 366 " ideal model delta sigma weight residual 1.529 1.471 0.058 1.64e-02 3.72e+03 1.24e+01 bond pdb=" C PHE A 363 " pdb=" N THR A 364 " ideal model delta sigma weight residual 1.331 1.286 0.045 1.30e-02 5.92e+03 1.21e+01 ... (remaining 8538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 11291 2.46 - 4.92: 236 4.92 - 7.38: 47 7.38 - 9.84: 7 9.84 - 12.30: 1 Bond angle restraints: 11582 Sorted by residual: angle pdb=" CA ASN A 292 " pdb=" CB ASN A 292 " pdb=" CG ASN A 292 " ideal model delta sigma weight residual 112.60 117.83 -5.23 1.00e+00 1.00e+00 2.74e+01 angle pdb=" C ASN A 371 " pdb=" CA ASN A 371 " pdb=" CB ASN A 371 " ideal model delta sigma weight residual 110.79 119.26 -8.47 1.66e+00 3.63e-01 2.61e+01 angle pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" O LEU A 291 " ideal model delta sigma weight residual 120.98 115.55 5.43 1.08e+00 8.57e-01 2.53e+01 angle pdb=" N LYS A 58 " pdb=" CA LYS A 58 " pdb=" C LYS A 58 " ideal model delta sigma weight residual 111.28 105.85 5.43 1.09e+00 8.42e-01 2.48e+01 angle pdb=" CA LYS A 53 " pdb=" C LYS A 53 " pdb=" O LYS A 53 " ideal model delta sigma weight residual 120.55 115.41 5.14 1.06e+00 8.90e-01 2.36e+01 ... (remaining 11577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 4988 24.18 - 48.37: 142 48.37 - 72.55: 17 72.55 - 96.74: 5 96.74 - 120.92: 2 Dihedral angle restraints: 5154 sinusoidal: 2048 harmonic: 3106 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 156.35 23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" C ASN A 371 " pdb=" N ASN A 371 " pdb=" CA ASN A 371 " pdb=" CB ASN A 371 " ideal model delta harmonic sigma weight residual -122.60 -133.51 10.91 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 5151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1158 0.083 - 0.166: 140 0.166 - 0.249: 14 0.249 - 0.332: 4 0.332 - 0.415: 3 Chirality restraints: 1319 Sorted by residual: chirality pdb=" CB VAL A 57 " pdb=" CA VAL A 57 " pdb=" CG1 VAL A 57 " pdb=" CG2 VAL A 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CBD Y01 R 501 " pdb=" CAK Y01 R 501 " pdb=" CBF Y01 R 501 " pdb=" CBG Y01 R 501 " both_signs ideal model delta sigma weight residual False 2.70 3.08 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CBH Y01 R 501 " pdb=" CAT Y01 R 501 " pdb=" CAZ Y01 R 501 " pdb=" CBF Y01 R 501 " both_signs ideal model delta sigma weight residual False -2.85 -2.50 -0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 1316 not shown) Planarity restraints: 1466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.076 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO B 39 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 19 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" C GLN A 19 " -0.051 2.00e-02 2.50e+03 pdb=" O GLN A 19 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG A 20 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 379 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" C CYS A 379 " 0.050 2.00e-02 2.50e+03 pdb=" O CYS A 379 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG A 380 " -0.017 2.00e-02 2.50e+03 ... (remaining 1463 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2212 2.81 - 3.33: 7561 3.33 - 3.85: 14649 3.85 - 4.38: 17459 4.38 - 4.90: 29652 Nonbonded interactions: 71533 Sorted by model distance: nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR B 289 " pdb=" O HOH B 401 " model vdw 2.347 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.349 3.040 nonbonded pdb=" O ALA B 248 " pdb=" O HOH B 402 " model vdw 2.350 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.356 3.040 ... (remaining 71528 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.800 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 37.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 0.081 8543 Z= 0.341 Angle : 0.884 12.300 11582 Z= 0.504 Chirality : 0.059 0.415 1319 Planarity : 0.007 0.117 1466 Dihedral : 12.161 120.919 3131 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.45 % Allowed : 1.12 % Favored : 98.44 % Cbeta Deviations : 0.10 % 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: -0.11 (0.25), residues: 1047 helix: -0.03 (0.24), residues: 408 sheet: 0.46 (0.34), residues: 232 loop : -0.23 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.007 0.002 HIS A 357 PHE 0.025 0.002 PHE R 185 TYR 0.015 0.002 TYR B 105 ARG 0.003 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7960 (mmt180) cc_final: 0.7650 (mtt90) REVERT: R 195 MET cc_start: 0.5437 (mtm) cc_final: 0.5005 (mtm) REVERT: R 237 TYR cc_start: 0.7736 (t80) cc_final: 0.7437 (t80) outliers start: 4 outliers final: 2 residues processed: 176 average time/residue: 1.7195 time to fit residues: 317.1306 Evaluate side-chains 144 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 390 GLN R 148 GLN R 207 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8543 Z= 0.249 Angle : 0.567 5.703 11582 Z= 0.308 Chirality : 0.043 0.148 1319 Planarity : 0.005 0.052 1466 Dihedral : 6.018 57.703 1231 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.01 % Allowed : 8.37 % Favored : 89.62 % 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: 1.24 (0.26), residues: 1047 helix: 1.92 (0.25), residues: 415 sheet: 0.64 (0.35), residues: 228 loop : -0.14 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.006 0.001 HIS B 311 PHE 0.016 0.002 PHE A 238 TYR 0.013 0.002 TYR B 105 ARG 0.007 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7803 (mptt) REVERT: A 389 ARG cc_start: 0.7842 (mmt180) cc_final: 0.7534 (tpp-160) REVERT: B 214 ARG cc_start: 0.7609 (mtt90) cc_final: 0.7392 (mtm180) REVERT: R 57 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.6142 (tp) REVERT: R 70 LYS cc_start: 0.7984 (mptt) cc_final: 0.7637 (mptt) REVERT: R 98 ASN cc_start: 0.6230 (m-40) cc_final: 0.5896 (m110) REVERT: R 195 MET cc_start: 0.5406 (mtm) cc_final: 0.5123 (mtm) REVERT: R 237 TYR cc_start: 0.7809 (t80) cc_final: 0.7543 (t80) outliers start: 18 outliers final: 4 residues processed: 158 average time/residue: 1.7118 time to fit residues: 283.0829 Evaluate side-chains 143 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 138 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 57 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 0.0870 chunk 25 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 390 GLN N 1 GLN R 148 GLN R 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8543 Z= 0.238 Angle : 0.553 10.110 11582 Z= 0.294 Chirality : 0.043 0.186 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.857 59.030 1231 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.56 % Allowed : 11.16 % Favored : 87.28 % 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: 1.62 (0.26), residues: 1047 helix: 2.43 (0.25), residues: 419 sheet: 0.59 (0.33), residues: 236 loop : -0.07 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.005 0.001 HIS B 311 PHE 0.014 0.002 PHE B 151 TYR 0.022 0.001 TYR R 179 ARG 0.008 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 1.120 Fit side-chains REVERT: A 17 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7812 (mptt) REVERT: A 389 ARG cc_start: 0.7817 (mmt180) cc_final: 0.7501 (tpp-160) REVERT: G 32 LYS cc_start: 0.8113 (tptm) cc_final: 0.7793 (tptp) REVERT: N 65 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8692 (ttmt) REVERT: R 70 LYS cc_start: 0.7925 (mptt) cc_final: 0.7601 (mptt) REVERT: R 98 ASN cc_start: 0.6280 (m-40) cc_final: 0.5943 (m110) REVERT: R 237 TYR cc_start: 0.7867 (t80) cc_final: 0.7620 (t80) REVERT: R 309 LYS cc_start: 0.8078 (mtmm) cc_final: 0.7845 (mttm) REVERT: R 338 TYR cc_start: 0.7727 (m-80) cc_final: 0.7440 (m-80) REVERT: R 375 LYS cc_start: 0.8225 (tptt) cc_final: 0.7893 (ttmm) outliers start: 14 outliers final: 8 residues processed: 154 average time/residue: 1.7168 time to fit residues: 276.3327 Evaluate side-chains 151 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 145 LYS Chi-restraints excluded: chain R residue 226 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 0.0770 chunk 99 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 89 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 390 GLN N 1 GLN R 148 GLN R 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8543 Z= 0.298 Angle : 0.572 6.683 11582 Z= 0.308 Chirality : 0.044 0.147 1319 Planarity : 0.004 0.047 1466 Dihedral : 5.887 58.555 1231 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.23 % Allowed : 11.50 % Favored : 86.27 % 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: 1.63 (0.26), residues: 1047 helix: 2.48 (0.25), residues: 420 sheet: 0.49 (0.33), residues: 241 loop : -0.05 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.006 0.001 HIS B 311 PHE 0.016 0.002 PHE B 151 TYR 0.024 0.002 TYR R 179 ARG 0.008 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 0.979 Fit side-chains REVERT: A 389 ARG cc_start: 0.7815 (mmt180) cc_final: 0.7517 (ttm110) REVERT: G 32 LYS cc_start: 0.8115 (tptm) cc_final: 0.7822 (tptp) REVERT: R 57 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6106 (tp) REVERT: R 98 ASN cc_start: 0.6303 (m-40) cc_final: 0.5969 (m110) REVERT: R 205 MET cc_start: 0.7327 (ptm) cc_final: 0.6809 (ptp) REVERT: R 237 TYR cc_start: 0.7910 (t80) cc_final: 0.7681 (t80) REVERT: R 338 TYR cc_start: 0.7723 (m-80) cc_final: 0.7495 (m-80) REVERT: R 375 LYS cc_start: 0.8183 (tptt) cc_final: 0.7880 (ttmm) outliers start: 20 outliers final: 8 residues processed: 158 average time/residue: 1.6686 time to fit residues: 275.7212 Evaluate side-chains 151 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 145 LYS Chi-restraints excluded: chain R residue 226 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 0.0770 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 68 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 390 GLN R 148 GLN R 207 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8543 Z= 0.141 Angle : 0.495 6.370 11582 Z= 0.262 Chirality : 0.041 0.158 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.505 59.054 1231 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.34 % Allowed : 13.39 % Favored : 85.27 % 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: 1.85 (0.26), residues: 1047 helix: 2.75 (0.25), residues: 419 sheet: 0.66 (0.34), residues: 224 loop : -0.04 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.002 0.001 HIS B 54 PHE 0.012 0.001 PHE B 199 TYR 0.017 0.001 TYR R 179 ARG 0.009 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 356 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7452 (mtt180) REVERT: A 370 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7143 (pp20) REVERT: A 389 ARG cc_start: 0.7697 (mmt180) cc_final: 0.7423 (ttm110) REVERT: G 32 LYS cc_start: 0.8014 (tptm) cc_final: 0.7764 (tptp) REVERT: N 65 LYS cc_start: 0.8886 (ttmt) cc_final: 0.8679 (ttmt) REVERT: R 57 LEU cc_start: 0.6441 (OUTLIER) cc_final: 0.5987 (tp) REVERT: R 70 LYS cc_start: 0.7960 (mptt) cc_final: 0.7625 (mptt) REVERT: R 98 ASN cc_start: 0.6306 (m-40) cc_final: 0.5985 (m110) REVERT: R 205 MET cc_start: 0.7289 (ptm) cc_final: 0.6967 (ptp) REVERT: R 237 TYR cc_start: 0.7877 (t80) cc_final: 0.7660 (t80) outliers start: 12 outliers final: 6 residues processed: 160 average time/residue: 1.6096 time to fit residues: 269.5307 Evaluate side-chains 150 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 145 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 8 optimal weight: 0.0050 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 390 GLN R 44 GLN R 148 GLN R 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8543 Z= 0.177 Angle : 0.530 8.795 11582 Z= 0.277 Chirality : 0.042 0.161 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.503 59.034 1231 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.01 % Allowed : 14.06 % Favored : 83.93 % 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: 1.88 (0.26), residues: 1047 helix: 2.75 (0.25), residues: 420 sheet: 0.62 (0.33), residues: 230 loop : 0.03 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.002 0.001 HIS A 362 PHE 0.011 0.001 PHE B 151 TYR 0.014 0.001 TYR R 179 ARG 0.008 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 356 ARG cc_start: 0.7709 (mtt180) cc_final: 0.7474 (mtt180) REVERT: A 370 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7163 (pp20) REVERT: A 389 ARG cc_start: 0.7694 (mmt180) cc_final: 0.7363 (ttm110) REVERT: G 32 LYS cc_start: 0.8033 (tptm) cc_final: 0.7783 (tptp) REVERT: N 65 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8680 (ttmt) REVERT: R 57 LEU cc_start: 0.6441 (OUTLIER) cc_final: 0.6082 (tp) REVERT: R 70 LYS cc_start: 0.7948 (mptt) cc_final: 0.7615 (mptt) REVERT: R 98 ASN cc_start: 0.6313 (m-40) cc_final: 0.5984 (m110) REVERT: R 205 MET cc_start: 0.7382 (ptm) cc_final: 0.7131 (ptp) REVERT: R 237 TYR cc_start: 0.7885 (t80) cc_final: 0.7670 (t80) outliers start: 18 outliers final: 8 residues processed: 156 average time/residue: 1.6383 time to fit residues: 267.9176 Evaluate side-chains 148 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 145 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 72 optimal weight: 0.0030 chunk 83 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 overall best weight: 0.4548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 390 GLN R 148 GLN R 207 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8543 Z= 0.141 Angle : 0.504 8.582 11582 Z= 0.263 Chirality : 0.041 0.172 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.344 59.869 1231 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.23 % Allowed : 13.62 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.26), residues: 1047 helix: 2.85 (0.25), residues: 420 sheet: 0.59 (0.33), residues: 228 loop : 0.04 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.001 0.001 HIS B 54 PHE 0.011 0.001 PHE B 199 TYR 0.011 0.001 TYR A 339 ARG 0.009 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7134 (pp20) REVERT: A 389 ARG cc_start: 0.7622 (mmt180) cc_final: 0.7334 (ttm110) REVERT: G 13 ARG cc_start: 0.7489 (mtm110) cc_final: 0.7288 (mtm110) REVERT: G 32 LYS cc_start: 0.7989 (tptm) cc_final: 0.7774 (tptp) REVERT: N 5 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7553 (tm-30) REVERT: N 65 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8656 (ttmt) REVERT: R 70 LYS cc_start: 0.7925 (mptt) cc_final: 0.7600 (mptt) REVERT: R 98 ASN cc_start: 0.6318 (m-40) cc_final: 0.5968 (m110) REVERT: R 237 TYR cc_start: 0.7856 (t80) cc_final: 0.7647 (t80) REVERT: R 309 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8070 (mttm) outliers start: 20 outliers final: 6 residues processed: 159 average time/residue: 1.6137 time to fit residues: 268.8028 Evaluate side-chains 153 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 309 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 67 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 390 GLN R 148 GLN R 207 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8543 Z= 0.180 Angle : 0.534 8.865 11582 Z= 0.281 Chirality : 0.042 0.174 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.419 59.551 1231 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.12 % Allowed : 14.29 % Favored : 83.59 % 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: 1.96 (0.26), residues: 1047 helix: 2.83 (0.25), residues: 421 sheet: 0.62 (0.33), residues: 230 loop : 0.07 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.002 0.001 HIS B 311 PHE 0.011 0.001 PHE A 212 TYR 0.012 0.001 TYR A 339 ARG 0.008 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 ARG cc_start: 0.7715 (mtt180) cc_final: 0.7241 (mtt-85) REVERT: A 370 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7177 (pp20) REVERT: A 389 ARG cc_start: 0.7649 (mmt180) cc_final: 0.7157 (ttm110) REVERT: G 13 ARG cc_start: 0.7525 (mtm110) cc_final: 0.7287 (mtm110) REVERT: N 65 LYS cc_start: 0.8897 (ttmt) cc_final: 0.8675 (ttmt) REVERT: R 70 LYS cc_start: 0.7932 (mptt) cc_final: 0.7611 (mptt) REVERT: R 98 ASN cc_start: 0.6393 (m-40) cc_final: 0.6028 (m110) REVERT: R 115 LYS cc_start: 0.7315 (mmtp) cc_final: 0.7114 (mmmt) REVERT: R 237 TYR cc_start: 0.7868 (t80) cc_final: 0.7654 (t80) REVERT: R 309 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8033 (mmtm) outliers start: 19 outliers final: 8 residues processed: 159 average time/residue: 1.6598 time to fit residues: 276.6622 Evaluate side-chains 154 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 309 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 0.0770 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 390 GLN R 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8543 Z= 0.165 Angle : 0.543 10.992 11582 Z= 0.283 Chirality : 0.041 0.178 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.391 59.746 1231 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.23 % Allowed : 15.18 % Favored : 83.59 % 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: 1.98 (0.26), residues: 1047 helix: 2.84 (0.25), residues: 422 sheet: 0.60 (0.33), residues: 230 loop : 0.11 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.002 0.001 HIS B 54 PHE 0.011 0.001 PHE B 199 TYR 0.012 0.001 TYR A 339 ARG 0.009 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 ARG cc_start: 0.7709 (mtt180) cc_final: 0.7252 (mtt-85) REVERT: A 370 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7173 (pp20) REVERT: A 389 ARG cc_start: 0.7643 (mmt180) cc_final: 0.7168 (ttm110) REVERT: B 6 GLN cc_start: 0.7752 (tm-30) cc_final: 0.7399 (tm-30) REVERT: G 13 ARG cc_start: 0.7537 (mtm110) cc_final: 0.7209 (mtm110) REVERT: N 65 LYS cc_start: 0.8888 (ttmt) cc_final: 0.8665 (ttmt) REVERT: R 70 LYS cc_start: 0.7963 (mptt) cc_final: 0.7630 (mptt) REVERT: R 98 ASN cc_start: 0.6418 (m-40) cc_final: 0.6053 (m110) REVERT: R 237 TYR cc_start: 0.7857 (t80) cc_final: 0.7636 (t80) outliers start: 11 outliers final: 6 residues processed: 154 average time/residue: 1.5136 time to fit residues: 243.6559 Evaluate side-chains 154 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 114 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 68 optimal weight: 0.0770 chunk 102 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 390 GLN R 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8543 Z= 0.269 Angle : 0.610 10.553 11582 Z= 0.320 Chirality : 0.044 0.187 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.606 58.787 1231 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.12 % Allowed : 15.40 % Favored : 83.48 % 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: 1.83 (0.26), residues: 1047 helix: 2.73 (0.25), residues: 420 sheet: 0.47 (0.33), residues: 239 loop : 0.05 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.004 0.001 HIS A 362 PHE 0.014 0.002 PHE B 151 TYR 0.014 0.002 TYR A 339 ARG 0.009 0.001 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7924 (tptt) cc_final: 0.7538 (mptt) REVERT: A 356 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7326 (mtt-85) REVERT: A 370 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7150 (pp20) REVERT: A 389 ARG cc_start: 0.7690 (mmt180) cc_final: 0.7134 (ttm110) REVERT: B 197 ARG cc_start: 0.7829 (mmp80) cc_final: 0.7616 (mmp80) REVERT: R 57 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.6062 (tp) REVERT: R 70 LYS cc_start: 0.7978 (mptt) cc_final: 0.7634 (mptt) REVERT: R 98 ASN cc_start: 0.6338 (m-40) cc_final: 0.5988 (m110) REVERT: R 205 MET cc_start: 0.7809 (ptt) cc_final: 0.7546 (ppp) REVERT: R 237 TYR cc_start: 0.7880 (t80) cc_final: 0.7647 (t80) outliers start: 10 outliers final: 7 residues processed: 156 average time/residue: 1.6762 time to fit residues: 273.5650 Evaluate side-chains 152 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 114 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 390 GLN R 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.133180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.093597 restraints weight = 10840.928| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.88 r_work: 0.3187 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8543 Z= 0.181 Angle : 0.575 11.172 11582 Z= 0.299 Chirality : 0.042 0.184 1319 Planarity : 0.004 0.050 1466 Dihedral : 5.468 59.215 1231 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.12 % Allowed : 15.62 % Favored : 83.26 % 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: 1.91 (0.26), residues: 1047 helix: 2.77 (0.25), residues: 422 sheet: 0.52 (0.33), residues: 235 loop : 0.11 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.002 0.001 HIS B 311 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR A 339 ARG 0.011 0.001 ARG G 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5473.23 seconds wall clock time: 98 minutes 41.37 seconds (5921.37 seconds total)