Starting phenix.real_space_refine on Thu Feb 13 03:24:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mbx_23749/02_2025/7mbx_23749.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mbx_23749/02_2025/7mbx_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/cci-nas-00/data/ceres_data/7mbx_23749/02_2025/7mbx_23749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mbx_23749/02_2025/7mbx_23749.map" model { file = "/net/cci-nas-00/data/ceres_data/7mbx_23749/02_2025/7mbx_23749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mbx_23749/02_2025/7mbx_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-5592/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: 5.64, per 1000 atoms: 0.67 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: 2.06 Conformation dependent library (CDL) restraints added in 1.2 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: 0.89 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: 2.44 Time building geometry restraints manager: 2.40 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: 1.390 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: 0.070 Process input model: 22.510 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 0.953 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: 1.7561 time to fit residues: 323.4928 Evaluate side-chains 144 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.132252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.092503 restraints weight = 10940.477| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.89 r_work: 0.3167 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 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 = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 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 to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8027 (ttmt) cc_final: 0.7498 (mptt) REVERT: A 389 ARG cc_start: 0.8207 (mmt180) cc_final: 0.7582 (tpp-160) REVERT: B 214 ARG cc_start: 0.8379 (mtt90) cc_final: 0.8026 (mtm180) REVERT: R 57 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5904 (tp) REVERT: R 70 LYS cc_start: 0.7821 (mptt) cc_final: 0.7459 (mptt) REVERT: R 98 ASN cc_start: 0.6032 (m-40) cc_final: 0.5674 (m110) REVERT: R 195 MET cc_start: 0.5098 (mtm) cc_final: 0.4805 (mtm) REVERT: R 237 TYR cc_start: 0.8111 (t80) cc_final: 0.7661 (t80) outliers start: 18 outliers final: 4 residues processed: 158 average time/residue: 1.7757 time to fit residues: 293.1721 Evaluate side-chains 143 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 18 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.133860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094204 restraints weight = 11006.766| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.89 r_work: 0.3194 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 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 = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8543 Z= 0.171 Angle : 0.515 9.686 11582 Z= 0.272 Chirality : 0.041 0.194 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.704 58.930 1231 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.45 % Allowed : 11.05 % Favored : 87.50 % 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: 1.69 (0.26), residues: 1047 helix: 2.53 (0.25), residues: 419 sheet: 0.59 (0.33), residues: 236 loop : -0.05 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.004 0.001 HIS B 311 PHE 0.011 0.001 PHE A 212 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 164 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7449 (mptt) REVERT: A 389 ARG cc_start: 0.8161 (mmt180) cc_final: 0.7588 (ttm110) REVERT: B 136 SER cc_start: 0.8976 (t) cc_final: 0.8775 (p) REVERT: G 32 LYS cc_start: 0.8327 (tptm) cc_final: 0.7941 (tptp) REVERT: R 70 LYS cc_start: 0.7775 (mptt) cc_final: 0.7458 (mptt) REVERT: R 98 ASN cc_start: 0.6040 (m-40) cc_final: 0.5665 (m110) REVERT: R 237 TYR cc_start: 0.8143 (t80) cc_final: 0.7708 (t80) REVERT: R 309 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7598 (mttm) REVERT: R 338 TYR cc_start: 0.7884 (m-80) cc_final: 0.7601 (m-80) outliers start: 13 outliers final: 6 residues processed: 157 average time/residue: 1.7630 time to fit residues: 289.6141 Evaluate side-chains 151 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 145 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.132135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.092321 restraints weight = 10862.103| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.88 r_work: 0.3163 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1971 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= 0.230 Angle : 0.538 6.513 11582 Z= 0.287 Chirality : 0.042 0.141 1319 Planarity : 0.004 0.047 1466 Dihedral : 5.735 59.106 1231 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.12 % Allowed : 11.50 % Favored : 86.38 % 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: 419 sheet: 0.54 (0.33), residues: 236 loop : -0.07 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.005 0.001 HIS B 311 PHE 0.014 0.002 PHE B 151 TYR 0.020 0.001 TYR R 179 ARG 0.007 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 171 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7514 (tptt) REVERT: A 389 ARG cc_start: 0.8162 (mmt180) cc_final: 0.7564 (ttm110) REVERT: G 32 LYS cc_start: 0.8345 (tptm) cc_final: 0.8002 (tptp) REVERT: R 45 ILE cc_start: 0.6709 (mt) cc_final: 0.6434 (tp) REVERT: R 70 LYS cc_start: 0.7824 (mptt) cc_final: 0.7467 (mptt) REVERT: R 98 ASN cc_start: 0.6130 (m-40) cc_final: 0.5747 (m110) REVERT: R 205 MET cc_start: 0.7075 (ptm) cc_final: 0.6493 (ptp) REVERT: R 207 GLN cc_start: 0.6971 (mt0) cc_final: 0.6769 (mt0) REVERT: R 237 TYR cc_start: 0.8163 (t80) cc_final: 0.7766 (t80) REVERT: R 338 TYR cc_start: 0.7834 (m-80) cc_final: 0.7630 (m-80) outliers start: 19 outliers final: 7 residues processed: 162 average time/residue: 1.7206 time to fit residues: 291.6427 Evaluate side-chains 155 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 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 58 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 45 optimal weight: 0.0570 chunk 69 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 0.0980 overall best weight: 0.5500 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.134774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.095416 restraints weight = 10853.678| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.86 r_work: 0.3220 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8543 Z= 0.145 Angle : 0.493 6.513 11582 Z= 0.260 Chirality : 0.040 0.148 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.466 59.143 1231 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.45 % Allowed : 13.50 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.26), residues: 1047 helix: 2.87 (0.25), residues: 418 sheet: 0.67 (0.33), residues: 230 loop : -0.05 (0.31), residues: 399 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 0.017 0.001 TYR R 179 ARG 0.008 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 167 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7963 (ttmt) cc_final: 0.7460 (tptt) REVERT: A 356 ARG cc_start: 0.8479 (mtt180) cc_final: 0.8115 (mtt180) REVERT: A 370 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7159 (pp20) REVERT: A 389 ARG cc_start: 0.8101 (mmt180) cc_final: 0.7500 (ttm110) REVERT: B 197 ARG cc_start: 0.8577 (mmp80) cc_final: 0.7912 (mmp80) REVERT: B 214 ARG cc_start: 0.8241 (mtt90) cc_final: 0.7848 (mtt90) REVERT: G 32 LYS cc_start: 0.8270 (tptm) cc_final: 0.7951 (tptp) REVERT: R 70 LYS cc_start: 0.7795 (mptt) cc_final: 0.7453 (mptt) REVERT: R 98 ASN cc_start: 0.6102 (m-40) cc_final: 0.5706 (m110) REVERT: R 205 MET cc_start: 0.7007 (ptm) cc_final: 0.6681 (ptp) REVERT: R 207 GLN cc_start: 0.6905 (mt0) cc_final: 0.6702 (mt0) REVERT: R 237 TYR cc_start: 0.8131 (t80) cc_final: 0.7730 (t80) REVERT: R 373 MET cc_start: 0.8612 (mtp) cc_final: 0.8399 (mtm) outliers start: 13 outliers final: 6 residues processed: 162 average time/residue: 1.7150 time to fit residues: 290.7272 Evaluate side-chains 157 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER 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 N residue 12 VAL Chi-restraints excluded: chain P residue 3 MET 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 101 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.133958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.094386 restraints weight = 10852.025| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.88 r_work: 0.3202 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 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 = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8543 Z= 0.165 Angle : 0.506 7.554 11582 Z= 0.268 Chirality : 0.041 0.156 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.449 59.177 1231 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.91 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: 2.00 (0.27), residues: 1047 helix: 2.88 (0.25), residues: 420 sheet: 0.65 (0.33), residues: 237 loop : 0.08 (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 0.011 0.001 PHE B 199 TYR 0.015 0.001 TYR R 179 ARG 0.009 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 172 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7450 (tptt) REVERT: A 370 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7189 (pp20) REVERT: A 389 ARG cc_start: 0.8076 (mmt180) cc_final: 0.7416 (ttm110) REVERT: G 13 ARG cc_start: 0.7734 (mtm110) cc_final: 0.7339 (mtm110) REVERT: G 32 LYS cc_start: 0.8273 (tptm) cc_final: 0.7999 (tptp) REVERT: R 57 LEU cc_start: 0.6111 (OUTLIER) cc_final: 0.5731 (tp) REVERT: R 70 LYS cc_start: 0.7771 (mptt) cc_final: 0.7433 (mptt) REVERT: R 98 ASN cc_start: 0.6145 (m-40) cc_final: 0.5715 (m110) REVERT: R 205 MET cc_start: 0.7101 (ptm) cc_final: 0.6867 (ptp) REVERT: R 237 TYR cc_start: 0.8129 (t80) cc_final: 0.7724 (t80) outliers start: 18 outliers final: 9 residues processed: 163 average time/residue: 1.7393 time to fit residues: 296.8841 Evaluate side-chains 156 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 57 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 88 optimal weight: 0.0270 chunk 100 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.134270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.094925 restraints weight = 10954.465| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.88 r_work: 0.3210 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8543 Z= 0.156 Angle : 0.503 7.851 11582 Z= 0.267 Chirality : 0.041 0.163 1319 Planarity : 0.004 0.047 1466 Dihedral : 5.396 59.575 1231 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.79 % Allowed : 14.29 % 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: 2.04 (0.27), residues: 1047 helix: 2.92 (0.25), residues: 420 sheet: 0.65 (0.33), residues: 236 loop : 0.09 (0.32), residues: 391 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 B 199 TYR 0.012 0.001 TYR R 179 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 165 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7444 (tptt) REVERT: A 356 ARG cc_start: 0.8479 (mtt180) cc_final: 0.8133 (mtt180) REVERT: A 370 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7195 (pp20) REVERT: A 389 ARG cc_start: 0.8079 (mmt180) cc_final: 0.7391 (ttm110) REVERT: B 197 ARG cc_start: 0.8673 (mmp80) cc_final: 0.8271 (mmp80) REVERT: G 32 LYS cc_start: 0.8251 (tptm) cc_final: 0.7978 (tptp) REVERT: N 5 GLN cc_start: 0.8645 (mm-40) cc_final: 0.7923 (tm-30) REVERT: R 45 ILE cc_start: 0.6690 (mt) cc_final: 0.6469 (tp) REVERT: R 70 LYS cc_start: 0.7754 (mptt) cc_final: 0.7423 (mptt) REVERT: R 98 ASN cc_start: 0.6149 (m-40) cc_final: 0.5713 (m110) REVERT: R 237 TYR cc_start: 0.8112 (t80) cc_final: 0.7704 (t80) REVERT: R 305 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7429 (tp) REVERT: R 309 LYS cc_start: 0.8143 (mtmm) cc_final: 0.7839 (mtmm) outliers start: 16 outliers final: 8 residues processed: 158 average time/residue: 1.7374 time to fit residues: 287.0664 Evaluate side-chains 155 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER 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 145 LYS Chi-restraints excluded: chain R residue 226 MET Chi-restraints excluded: chain R residue 305 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.133527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.093983 restraints weight = 11015.333| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.89 r_work: 0.3192 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 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 = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8543 Z= 0.180 Angle : 0.517 7.291 11582 Z= 0.276 Chirality : 0.041 0.163 1319 Planarity : 0.004 0.047 1466 Dihedral : 5.451 59.655 1231 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.90 % Allowed : 13.84 % Favored : 84.26 % 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: 1.99 (0.26), residues: 1047 helix: 2.92 (0.25), residues: 420 sheet: 0.60 (0.33), residues: 232 loop : 0.04 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.003 0.001 HIS B 311 PHE 0.011 0.001 PHE A 212 TYR 0.013 0.001 TYR R 179 ARG 0.010 0.001 ARG G 13 *********************** 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 to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7954 (ttmt) cc_final: 0.7438 (tptt) REVERT: A 356 ARG cc_start: 0.8495 (mtt180) cc_final: 0.8139 (mtt180) REVERT: A 370 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7196 (pp20) REVERT: A 389 ARG cc_start: 0.8091 (mmt180) cc_final: 0.7377 (ttm110) REVERT: B 197 ARG cc_start: 0.8597 (mmp80) cc_final: 0.7923 (mmp80) REVERT: B 214 ARG cc_start: 0.8195 (mtm180) cc_final: 0.7823 (mtm180) REVERT: G 13 ARG cc_start: 0.7716 (mtm110) cc_final: 0.7319 (mtm110) REVERT: G 32 LYS cc_start: 0.8262 (tptm) cc_final: 0.8021 (tptp) REVERT: R 70 LYS cc_start: 0.7777 (mptt) cc_final: 0.7444 (mptt) REVERT: R 98 ASN cc_start: 0.6153 (m-40) cc_final: 0.5724 (m110) REVERT: R 205 MET cc_start: 0.7506 (ptp) cc_final: 0.7265 (ptt) REVERT: R 237 TYR cc_start: 0.8131 (t80) cc_final: 0.7726 (t80) REVERT: R 309 LYS cc_start: 0.8159 (mtmm) cc_final: 0.7880 (mtmm) outliers start: 17 outliers final: 11 residues processed: 160 average time/residue: 1.7570 time to fit residues: 294.3817 Evaluate side-chains 159 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 349 SER 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 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 91 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 80 optimal weight: 0.3980 chunk 54 optimal weight: 0.0010 chunk 95 optimal weight: 6.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN N 1 GLN R 44 GLN R 148 GLN R 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.134300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.095076 restraints weight = 11092.749| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.89 r_work: 0.3212 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8543 Z= 0.156 Angle : 0.517 8.053 11582 Z= 0.274 Chirality : 0.041 0.179 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.389 59.789 1231 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.90 % Allowed : 14.29 % 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: 2.02 (0.26), residues: 1047 helix: 2.95 (0.25), residues: 419 sheet: 0.58 (0.33), residues: 237 loop : 0.08 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 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 0.000 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 164 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7422 (tptt) REVERT: A 356 ARG cc_start: 0.8480 (mtt180) cc_final: 0.8123 (mtt180) REVERT: A 370 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7175 (pp20) REVERT: A 389 ARG cc_start: 0.8062 (mmt180) cc_final: 0.7355 (ttm110) REVERT: B 197 ARG cc_start: 0.8515 (mmp80) cc_final: 0.8089 (mmp80) REVERT: G 13 ARG cc_start: 0.7693 (mtm110) cc_final: 0.7413 (mtm110) REVERT: G 32 LYS cc_start: 0.8232 (tptm) cc_final: 0.8014 (tptp) REVERT: N 5 GLN cc_start: 0.8635 (mm-40) cc_final: 0.7920 (tm-30) REVERT: R 70 LYS cc_start: 0.7782 (mptt) cc_final: 0.7448 (mptt) REVERT: R 98 ASN cc_start: 0.6152 (m-40) cc_final: 0.5731 (m110) REVERT: R 205 MET cc_start: 0.7565 (ptp) cc_final: 0.7345 (ptt) REVERT: R 237 TYR cc_start: 0.8121 (t80) cc_final: 0.7720 (t80) outliers start: 17 outliers final: 9 residues processed: 157 average time/residue: 1.7093 time to fit residues: 280.6695 Evaluate side-chains 152 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER 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 89 MET Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 226 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 32 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.132909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.093414 restraints weight = 10899.396| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.87 r_work: 0.3183 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 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 = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 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 : 0.003 0.034 8543 Z= 0.199 Angle : 0.557 10.616 11582 Z= 0.291 Chirality : 0.042 0.175 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.494 59.528 1231 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: 1.92 (0.26), residues: 1047 helix: 2.85 (0.25), residues: 419 sheet: 0.57 (0.33), residues: 232 loop : 0.02 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.003 0.001 HIS B 311 PHE 0.011 0.001 PHE B 151 TYR 0.013 0.001 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 158 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7455 (tptt) REVERT: A 370 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7198 (pp20) REVERT: A 389 ARG cc_start: 0.8065 (mmt180) cc_final: 0.7392 (ttm110) REVERT: G 13 ARG cc_start: 0.7754 (mtm110) cc_final: 0.7461 (mtm110) REVERT: G 32 LYS cc_start: 0.8264 (tptm) cc_final: 0.8022 (tptp) REVERT: R 57 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5728 (tp) REVERT: R 70 LYS cc_start: 0.7793 (mptt) cc_final: 0.7453 (mptt) REVERT: R 98 ASN cc_start: 0.6202 (m-40) cc_final: 0.5812 (m110) REVERT: R 205 MET cc_start: 0.7662 (ptp) cc_final: 0.7417 (ptt) REVERT: R 237 TYR cc_start: 0.8111 (t80) cc_final: 0.7706 (t80) outliers start: 14 outliers final: 10 residues processed: 153 average time/residue: 1.7847 time to fit residues: 285.5279 Evaluate side-chains 156 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 349 SER 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 Chi-restraints excluded: chain R residue 226 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 36 optimal weight: 0.0570 chunk 81 optimal weight: 9.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.134600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.095402 restraints weight = 11101.446| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.89 r_work: 0.3218 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2418 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= 0.150 Angle : 0.535 11.910 11582 Z= 0.276 Chirality : 0.041 0.186 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.371 59.582 1231 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.34 % Allowed : 15.40 % 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: 1.99 (0.26), residues: 1047 helix: 2.92 (0.25), residues: 418 sheet: 0.56 (0.33), residues: 236 loop : 0.07 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 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 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17915.57 seconds wall clock time: 313 minutes 30.75 seconds (18810.75 seconds total)