Starting phenix.real_space_refine on Mon Mar 11 14:09:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbx_23749/03_2024/7mbx_23749.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbx_23749/03_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_23749/03_2024/7mbx_23749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbx_23749/03_2024/7mbx_23749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbx_23749/03_2024/7mbx_23749.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbx_23749/03_2024/7mbx_23749.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8433 Number of models: 1 Model: "" Number of chains: 11 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'NH2': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, '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: "R" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2339 Unusual residues: {'Y01': 1} Classifications: {'peptide': 292, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 278, None: 1} Not linked: pdbres="PRO R 386 " pdbres="Y01 R 501 " 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: "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: 5.56, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 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: 3.11 Conformation dependent library (CDL) restraints added in 1.9 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: 0.91 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: 2.91 Time building geometry restraints manager: 3.43 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: 2329 1.44 - 1.56: 4766 1.56 - 1.69: 5 1.69 - 1.82: 92 Bond restraints: 8544 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 8539 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.58: 151 105.58 - 112.71: 4434 112.71 - 119.84: 3011 119.84 - 126.97: 3887 126.97 - 134.10: 101 Bond angle restraints: 11584 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 11579 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: 1467 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 1464 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 2.440 nonbonded pdb=" OH TYR B 289 " pdb=" O HOH B 401 " model vdw 2.347 2.440 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.349 2.440 nonbonded pdb=" O ALA B 248 " pdb=" O HOH B 402 " model vdw 2.350 2.440 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.356 2.440 ... (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 ========== 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: 1.170 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: 5.480 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.800 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.540 ------------------------------------------------------------------------------- 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 8544 Z= 0.335 Angle : 0.884 12.300 11584 Z= 0.504 Chirality : 0.059 0.415 1319 Planarity : 0.007 0.117 1467 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 : 1.084 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: 1.6643 time to fit residues: 306.3759 Evaluate side-chains 144 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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: 3.9990 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 0.3980 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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: 0.8365 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8544 Z= 0.195 Angle : 0.526 5.689 11584 Z= 0.283 Chirality : 0.042 0.144 1319 Planarity : 0.005 0.051 1467 Dihedral : 5.908 58.238 1231 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.67 % Allowed : 9.15 % Favored : 89.17 % 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 (0.26), residues: 1047 helix: 1.98 (0.25), residues: 414 sheet: 0.73 (0.34), residues: 232 loop : -0.18 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.006 0.001 HIS B 311 PHE 0.014 0.002 PHE R 212 TYR 0.012 0.001 TYR R 179 ARG 0.008 0.001 ARG A 385 *********************** 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 163 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7840 (mmt180) cc_final: 0.7560 (ttm110) REVERT: B 6 GLN cc_start: 0.7693 (tm-30) cc_final: 0.7439 (tm-30) REVERT: G 32 LYS cc_start: 0.7975 (tptm) cc_final: 0.7675 (tptp) REVERT: R 57 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6123 (tp) REVERT: R 70 LYS cc_start: 0.7965 (mptt) cc_final: 0.7628 (mptt) REVERT: R 195 MET cc_start: 0.5361 (mtm) cc_final: 0.5042 (mtm) REVERT: R 237 TYR cc_start: 0.7816 (t80) cc_final: 0.7547 (t80) outliers start: 15 outliers final: 6 residues processed: 157 average time/residue: 1.7075 time to fit residues: 280.8703 Evaluate side-chains 143 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 357 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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: 0.8431 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8544 Z= 0.404 Angle : 0.636 9.758 11584 Z= 0.340 Chirality : 0.047 0.180 1319 Planarity : 0.005 0.047 1467 Dihedral : 6.098 59.510 1231 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.79 % Allowed : 11.16 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.44 (0.26), residues: 1047 helix: 2.16 (0.25), residues: 420 sheet: 0.60 (0.34), residues: 241 loop : -0.09 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.009 0.002 HIS B 311 PHE 0.020 0.002 PHE B 151 TYR 0.023 0.002 TYR R 179 ARG 0.007 0.001 ARG N 19 *********************** 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 160 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7830 (mptt) cc_final: 0.7466 (tptt) REVERT: A 389 ARG cc_start: 0.7885 (mmt180) cc_final: 0.7495 (ttm110) REVERT: G 32 LYS cc_start: 0.8120 (tptm) cc_final: 0.7675 (tptp) REVERT: R 57 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.6100 (tp) REVERT: R 70 LYS cc_start: 0.7933 (mptt) cc_final: 0.7613 (mptt) REVERT: R 237 TYR cc_start: 0.7919 (t80) cc_final: 0.7672 (t80) REVERT: R 309 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7724 (mttm) REVERT: R 375 LYS cc_start: 0.8140 (tptt) cc_final: 0.7786 (ttmm) outliers start: 16 outliers final: 8 residues processed: 153 average time/residue: 1.7091 time to fit residues: 273.5019 Evaluate side-chains 146 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain R residue 357 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 94 optimal weight: 0.0270 chunk 99 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 30.0000 chunk 26 optimal weight: 4.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- 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: 0.8393 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8544 Z= 0.208 Angle : 0.526 7.192 11584 Z= 0.281 Chirality : 0.042 0.139 1319 Planarity : 0.004 0.046 1467 Dihedral : 5.768 59.311 1231 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.90 % Allowed : 12.17 % Favored : 85.94 % 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: 1.73 (0.26), residues: 1047 helix: 2.57 (0.26), residues: 419 sheet: 0.64 (0.34), residues: 237 loop : -0.06 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.004 0.001 HIS B 311 PHE 0.012 0.001 PHE B 151 TYR 0.021 0.001 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 161 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.028 Fit side-chains REVERT: A 356 ARG cc_start: 0.7683 (mtt180) cc_final: 0.7474 (mtt180) REVERT: A 389 ARG cc_start: 0.7834 (mmt180) cc_final: 0.7482 (ttm110) REVERT: G 32 LYS cc_start: 0.8013 (tptm) cc_final: 0.7639 (tptp) REVERT: R 57 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.6096 (tp) REVERT: R 70 LYS cc_start: 0.7971 (mptt) cc_final: 0.7659 (mptt) REVERT: R 205 MET cc_start: 0.7226 (ptm) cc_final: 0.6752 (ptt) REVERT: R 237 TYR cc_start: 0.7900 (t80) cc_final: 0.7672 (t80) REVERT: R 373 MET cc_start: 0.8585 (mtp) cc_final: 0.8379 (mtm) REVERT: R 375 LYS cc_start: 0.8078 (tptt) cc_final: 0.7832 (ttmm) outliers start: 17 outliers final: 5 residues processed: 154 average time/residue: 1.7392 time to fit residues: 279.9306 Evaluate side-chains 146 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 57 LEU Chi-restraints excluded: chain R residue 89 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 0.0970 chunk 84 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8369 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8544 Z= 0.163 Angle : 0.499 6.588 11584 Z= 0.265 Chirality : 0.041 0.148 1319 Planarity : 0.004 0.046 1467 Dihedral : 5.534 58.376 1231 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.67 % Allowed : 13.06 % 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: 1.92 (0.27), residues: 1047 helix: 2.75 (0.26), residues: 419 sheet: 0.71 (0.33), residues: 235 loop : 0.04 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.002 0.001 HIS B 311 PHE 0.013 0.001 PHE B 199 TYR 0.016 0.001 TYR R 179 ARG 0.008 0.000 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 159 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7752 (mptt) cc_final: 0.7299 (mmmt) REVERT: A 370 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7156 (pp20) REVERT: A 389 ARG cc_start: 0.7775 (mmt180) cc_final: 0.7414 (ttm110) REVERT: B 197 ARG cc_start: 0.7864 (mmp80) cc_final: 0.7560 (mmp80) REVERT: G 13 ARG cc_start: 0.7647 (mtm110) cc_final: 0.7406 (mtm110) REVERT: G 32 LYS cc_start: 0.7954 (tptm) cc_final: 0.7588 (tptp) REVERT: R 70 LYS cc_start: 0.7967 (mptt) cc_final: 0.7637 (mptt) REVERT: R 205 MET cc_start: 0.7255 (ptm) cc_final: 0.6937 (ptp) REVERT: R 219 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8242 (mm) REVERT: R 237 TYR cc_start: 0.7903 (t80) cc_final: 0.7681 (t80) REVERT: R 373 MET cc_start: 0.8577 (mtp) cc_final: 0.8376 (mtm) outliers start: 15 outliers final: 7 residues processed: 150 average time/residue: 1.7391 time to fit residues: 272.4857 Evaluate side-chains 147 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 G residue 46 LYS 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 219 LEU Chi-restraints excluded: chain R residue 226 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 30.0000 chunk 19 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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: 0.8390 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8544 Z= 0.218 Angle : 0.525 6.937 11584 Z= 0.280 Chirality : 0.042 0.157 1319 Planarity : 0.004 0.046 1467 Dihedral : 5.587 58.169 1231 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.01 % Allowed : 13.84 % 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: 1.86 (0.26), residues: 1047 helix: 2.74 (0.25), residues: 419 sheet: 0.63 (0.33), residues: 237 loop : -0.01 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.003 0.001 HIS B 311 PHE 0.012 0.001 PHE B 151 TYR 0.014 0.001 TYR R 179 ARG 0.008 0.001 ARG A 61 *********************** 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 160 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7753 (mptt) cc_final: 0.7309 (mmmt) REVERT: A 370 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7144 (pp20) REVERT: A 389 ARG cc_start: 0.7740 (mmt180) cc_final: 0.7396 (ttm110) REVERT: G 13 ARG cc_start: 0.7692 (mtm110) cc_final: 0.7470 (mtm110) REVERT: G 32 LYS cc_start: 0.7980 (tptm) cc_final: 0.7660 (tptp) REVERT: R 70 LYS cc_start: 0.7938 (mptt) cc_final: 0.7614 (mptt) REVERT: R 205 MET cc_start: 0.7353 (ptm) cc_final: 0.7101 (ptp) REVERT: R 237 TYR cc_start: 0.7903 (t80) cc_final: 0.7688 (t80) REVERT: R 373 MET cc_start: 0.8615 (mtp) cc_final: 0.8407 (mtm) outliers start: 18 outliers final: 8 residues processed: 153 average time/residue: 1.6612 time to fit residues: 266.0261 Evaluate side-chains 148 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 139 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 B residue 214 ARG 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 226 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 61 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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: 0.8363 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8544 Z= 0.155 Angle : 0.494 6.887 11584 Z= 0.263 Chirality : 0.041 0.164 1319 Planarity : 0.004 0.046 1467 Dihedral : 5.406 58.928 1231 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.67 % Allowed : 14.17 % 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: 1.97 (0.26), residues: 1047 helix: 2.87 (0.26), residues: 419 sheet: 0.69 (0.33), residues: 230 loop : 0.00 (0.31), residues: 398 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 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR A 339 ARG 0.009 0.000 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 158 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7752 (mptt) cc_final: 0.7295 (mmmt) REVERT: A 356 ARG cc_start: 0.7699 (mtt180) cc_final: 0.7320 (mtt-85) REVERT: A 370 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7167 (pp20) REVERT: A 389 ARG cc_start: 0.7673 (mmt180) cc_final: 0.7147 (ttm110) REVERT: G 13 ARG cc_start: 0.7679 (mtm110) cc_final: 0.7443 (mtm110) REVERT: G 32 LYS cc_start: 0.7918 (tptm) cc_final: 0.7592 (tptp) REVERT: R 70 LYS cc_start: 0.7931 (mptt) cc_final: 0.7614 (mptt) REVERT: R 145 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8182 (mtpm) REVERT: R 237 TYR cc_start: 0.7893 (t80) cc_final: 0.7677 (t80) outliers start: 15 outliers final: 7 residues processed: 151 average time/residue: 1.6932 time to fit residues: 267.6438 Evaluate side-chains 149 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 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 145 LYS Chi-restraints excluded: chain R residue 217 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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: 0.8393 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8544 Z= 0.233 Angle : 0.540 7.511 11584 Z= 0.289 Chirality : 0.043 0.169 1319 Planarity : 0.004 0.046 1467 Dihedral : 5.549 58.316 1231 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.90 % Allowed : 14.17 % 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: 1.86 (0.26), residues: 1047 helix: 2.78 (0.25), residues: 419 sheet: 0.61 (0.33), residues: 237 loop : -0.04 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.004 0.001 HIS B 311 PHE 0.013 0.001 PHE B 151 TYR 0.013 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 159 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7763 (mptt) cc_final: 0.7318 (mmmt) REVERT: A 356 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7310 (mtt-85) REVERT: A 370 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7156 (pp20) REVERT: A 389 ARG cc_start: 0.7736 (mmt180) cc_final: 0.7157 (ttm110) REVERT: G 32 LYS cc_start: 0.7971 (tptm) cc_final: 0.7652 (tptp) REVERT: R 57 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.6062 (tp) REVERT: R 70 LYS cc_start: 0.7940 (mptt) cc_final: 0.7621 (mptt) REVERT: R 145 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8231 (mtpm) REVERT: R 237 TYR cc_start: 0.7898 (t80) cc_final: 0.7680 (t80) outliers start: 17 outliers final: 9 residues processed: 152 average time/residue: 1.7082 time to fit residues: 271.6585 Evaluate side-chains 152 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL 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 89 MET Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 145 LYS Chi-restraints excluded: chain R residue 226 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8366 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8544 Z= 0.167 Angle : 0.514 7.434 11584 Z= 0.274 Chirality : 0.041 0.182 1319 Planarity : 0.004 0.046 1467 Dihedral : 5.400 58.932 1231 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.45 % Allowed : 14.62 % 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: 1.98 (0.26), residues: 1047 helix: 2.88 (0.25), residues: 420 sheet: 0.64 (0.33), residues: 235 loop : 0.04 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.002 0.001 HIS B 311 PHE 0.011 0.001 PHE B 199 TYR 0.012 0.001 TYR A 339 ARG 0.009 0.001 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 154 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7741 (mptt) cc_final: 0.7295 (mmmt) REVERT: A 356 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7323 (mtt-85) REVERT: A 370 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7176 (pp20) REVERT: A 389 ARG cc_start: 0.7666 (mmt180) cc_final: 0.7093 (ttm110) REVERT: G 20 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8589 (mtmm) REVERT: G 32 LYS cc_start: 0.7911 (tptm) cc_final: 0.7597 (tptp) REVERT: R 70 LYS cc_start: 0.7939 (mptt) cc_final: 0.7628 (mptt) REVERT: R 145 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8209 (mtpm) REVERT: R 237 TYR cc_start: 0.7890 (t80) cc_final: 0.7676 (t80) REVERT: R 309 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7771 (mttm) outliers start: 13 outliers final: 8 residues processed: 148 average time/residue: 1.7131 time to fit residues: 265.0244 Evaluate side-chains 149 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 G residue 46 LYS 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 145 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8544 Z= 0.302 Angle : 0.594 8.508 11584 Z= 0.318 Chirality : 0.045 0.183 1319 Planarity : 0.004 0.046 1467 Dihedral : 5.686 58.007 1231 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.56 % Allowed : 14.96 % 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: 1.75 (0.26), residues: 1047 helix: 2.66 (0.25), residues: 418 sheet: 0.56 (0.33), residues: 237 loop : -0.08 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.005 0.001 HIS A 362 PHE 0.015 0.002 PHE B 151 TYR 0.015 0.002 TYR A 339 ARG 0.011 0.001 ARG G 13 ********************** 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 155 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7780 (mptt) cc_final: 0.7319 (mmmt) REVERT: A 356 ARG cc_start: 0.7741 (mtt180) cc_final: 0.7301 (mtt-85) REVERT: A 370 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7175 (pp20) REVERT: A 389 ARG cc_start: 0.7748 (mmt180) cc_final: 0.7105 (ttm110) REVERT: G 13 ARG cc_start: 0.7602 (mtm110) cc_final: 0.7399 (mtm110) REVERT: G 32 LYS cc_start: 0.8003 (tptm) cc_final: 0.7686 (tptp) REVERT: R 70 LYS cc_start: 0.7971 (mptt) cc_final: 0.7642 (mptt) REVERT: R 145 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8297 (mtpm) REVERT: R 205 MET cc_start: 0.7727 (ptt) cc_final: 0.7417 (ppp) REVERT: R 237 TYR cc_start: 0.7908 (t80) cc_final: 0.7686 (t80) REVERT: R 309 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7745 (mttm) outliers start: 14 outliers final: 8 residues processed: 150 average time/residue: 1.7612 time to fit residues: 275.9877 Evaluate side-chains 146 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL 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 89 MET Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 145 LYS 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: 2.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.132854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.093510 restraints weight = 10817.492| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.88 r_work: 0.3179 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8544 Z= 0.173 Angle : 0.532 8.293 11584 Z= 0.282 Chirality : 0.042 0.182 1319 Planarity : 0.004 0.047 1467 Dihedral : 5.428 58.850 1231 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.56 % Allowed : 14.62 % Favored : 83.82 % 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: 1.92 (0.26), residues: 1047 helix: 2.84 (0.25), residues: 418 sheet: 0.64 (0.33), residues: 235 loop : -0.01 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 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: 5481.66 seconds wall clock time: 96 minutes 47.83 seconds (5807.83 seconds total)