Starting phenix.real_space_refine on Wed Apr 30 22:03:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lyc_63523/04_2025/9lyc_63523_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lyc_63523/04_2025/9lyc_63523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lyc_63523/04_2025/9lyc_63523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lyc_63523/04_2025/9lyc_63523.map" model { file = "/net/cci-nas-00/data/ceres_data/9lyc_63523/04_2025/9lyc_63523_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lyc_63523/04_2025/9lyc_63523_neut.cif" } resolution = 3.06 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= 0.002 sd= 0.029 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 73 5.16 5 C 6430 2.51 5 N 1724 2.21 5 O 1829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10056 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2053 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 259} Chain breaks: 1 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: "C" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1940 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 231} 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: "D" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2072 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR: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: 971 Number of conformers: 1 Conformer: "" 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 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N SER N 127 " occ=0.94 ... (3 atoms not shown) pdb=" CB SER N 127 " occ=0.94 Time building chain proxies: 6.90, per 1000 atoms: 0.69 Number of scatterers: 10056 At special positions: 0 Unit cell: (79.872, 106.496, 146.432, 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 73 16.00 O 1829 8.00 N 1724 7.00 C 6430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS D 177 " - pdb=" SG CYS D 184 " distance=2.03 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2452 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 50.5% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 41 through 68 removed outlier: 3.724A pdb=" N VAL A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 60 " --> pdb=" O CYS A 56 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 101 removed outlier: 3.752A pdb=" N LEU A 78 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 79 " --> pdb=" O MET A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 140 Processing helix chain 'A' and resid 146 through 168 removed outlier: 3.699A pdb=" N VAL A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.800A pdb=" N ALA A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 232 Processing helix chain 'A' and resid 242 through 270 Proline residue: A 262 - end of helix Processing helix chain 'A' and resid 276 through 282 removed outlier: 4.226A pdb=" N TYR A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 298 removed outlier: 3.519A pdb=" N THR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Proline residue: A 294 - end of helix Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.511A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.749A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 40 removed outlier: 4.428A pdb=" N GLU C 15 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 213 through 217 removed outlier: 3.769A pdb=" N LYS C 216 " --> pdb=" O GLN C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 239 removed outlier: 3.722A pdb=" N GLN C 236 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN C 239 " --> pdb=" O GLN C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 279 removed outlier: 3.843A pdb=" N ALA C 268 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 304 Processing helix chain 'C' and resid 307 through 312 removed outlier: 4.454A pdb=" N TYR C 311 " --> pdb=" O LYS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 352 removed outlier: 3.633A pdb=" N ARG C 342 " --> pdb=" O LYS C 338 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 391 removed outlier: 3.508A pdb=" N ARG C 374 " --> pdb=" O GLU C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 68 removed outlier: 3.577A pdb=" N THR D 68 " --> pdb=" O ILE D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 102 removed outlier: 3.887A pdb=" N LEU D 78 " --> pdb=" O PRO D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 143 removed outlier: 3.657A pdb=" N SER D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR D 143 " --> pdb=" O TYR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 164 removed outlier: 3.564A pdb=" N ARG D 152 " --> pdb=" O THR D 148 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR D 154 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D 159 " --> pdb=" O VAL D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 170 Processing helix chain 'D' and resid 176 through 181 removed outlier: 3.619A pdb=" N GLY D 180 " --> pdb=" O ASN D 176 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU D 181 " --> pdb=" O CYS D 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 176 through 181' Processing helix chain 'D' and resid 191 through 223 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 242 through 270 removed outlier: 4.099A pdb=" N THR D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA D 250 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N CYS D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Proline residue: D 262 - end of helix removed outlier: 3.950A pdb=" N TYR D 266 " --> pdb=" O PRO D 262 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 298 removed outlier: 3.716A pdb=" N THR D 279 " --> pdb=" O PRO D 275 " (cutoff:3.500A) Proline residue: D 285 - end of helix Proline residue: D 294 - end of helix Processing helix chain 'D' and resid 301 through 314 Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.513A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.858A 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: 3.671A 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 87 through 91 removed outlier: 3.607A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.252A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.909A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.405A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.570A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.212A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.615A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.341A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 207 through 211 removed outlier: 3.762A pdb=" N PHE C 208 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS C 41 " --> pdb=" O HIS C 220 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N PHE C 222 " --> pdb=" O HIS C 41 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 43 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N VAL C 224 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LEU C 45 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG C 42 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE C 245 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU C 44 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL C 247 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU C 46 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ALA C 249 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE C 244 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N PHE C 290 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE C 246 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN C 292 " --> pdb=" O PHE C 246 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL C 248 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.797A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 5.895A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1683 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: 2.90 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2391 1.33 - 1.45: 2127 1.45 - 1.57: 5643 1.57 - 1.70: 0 1.70 - 1.82: 101 Bond restraints: 10262 Sorted by residual: bond pdb=" CA LYS B 89 " pdb=" C LYS B 89 " ideal model delta sigma weight residual 1.522 1.472 0.049 1.22e-02 6.72e+03 1.65e+01 bond pdb=" N VAL B 90 " pdb=" CA VAL B 90 " ideal model delta sigma weight residual 1.459 1.429 0.030 1.25e-02 6.40e+03 5.62e+00 bond pdb=" CA VAL B 90 " pdb=" CB VAL B 90 " ideal model delta sigma weight residual 1.540 1.510 0.031 1.36e-02 5.41e+03 5.03e+00 bond pdb=" C HIS B 91 " pdb=" O HIS B 91 " ideal model delta sigma weight residual 1.235 1.209 0.026 1.18e-02 7.18e+03 4.90e+00 bond pdb=" C LYS B 89 " pdb=" N VAL B 90 " ideal model delta sigma weight residual 1.332 1.304 0.028 1.36e-02 5.41e+03 4.15e+00 ... (remaining 10257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 13767 2.42 - 4.84: 154 4.84 - 7.26: 27 7.26 - 9.68: 9 9.68 - 12.10: 2 Bond angle restraints: 13959 Sorted by residual: angle pdb=" N LYS B 89 " pdb=" CA LYS B 89 " pdb=" C LYS B 89 " ideal model delta sigma weight residual 109.40 102.65 6.75 1.63e+00 3.76e-01 1.71e+01 angle pdb=" CA PRO A 74 " pdb=" N PRO A 74 " pdb=" CD PRO A 74 " ideal model delta sigma weight residual 112.00 106.77 5.23 1.40e+00 5.10e-01 1.40e+01 angle pdb=" CA MET D 118 " pdb=" CB MET D 118 " pdb=" CG MET D 118 " ideal model delta sigma weight residual 114.10 121.25 -7.15 2.00e+00 2.50e-01 1.28e+01 angle pdb=" C HIS B 91 " pdb=" N ALA B 92 " pdb=" CA ALA B 92 " ideal model delta sigma weight residual 122.77 127.89 -5.12 1.48e+00 4.57e-01 1.20e+01 angle pdb=" CA LEU D 95 " pdb=" CB LEU D 95 " pdb=" CG LEU D 95 " ideal model delta sigma weight residual 116.30 128.40 -12.10 3.50e+00 8.16e-02 1.19e+01 ... (remaining 13954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 5200 15.92 - 31.84: 644 31.84 - 47.76: 194 47.76 - 63.69: 34 63.69 - 79.61: 9 Dihedral angle restraints: 6081 sinusoidal: 2280 harmonic: 3801 Sorted by residual: dihedral pdb=" CA LYS G 20 " pdb=" C LYS G 20 " pdb=" N MET G 21 " pdb=" CA MET G 21 " ideal model delta harmonic sigma weight residual 180.00 158.73 21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA TRP B 297 " pdb=" C TRP B 297 " pdb=" N ASP B 298 " pdb=" CA ASP B 298 " ideal model delta harmonic sigma weight residual -180.00 -159.52 -20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ASP D 179 " pdb=" C ASP D 179 " pdb=" N GLY D 180 " pdb=" CA GLY D 180 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 6078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1096 0.036 - 0.072: 395 0.072 - 0.108: 107 0.108 - 0.144: 31 0.144 - 0.180: 8 Chirality restraints: 1637 Sorted by residual: chirality pdb=" CB VAL B 90 " pdb=" CA VAL B 90 " pdb=" CG1 VAL B 90 " pdb=" CG2 VAL B 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CB VAL A 115 " pdb=" CA VAL A 115 " pdb=" CG1 VAL A 115 " pdb=" CG2 VAL A 115 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA THR B 87 " pdb=" N THR B 87 " pdb=" C THR B 87 " pdb=" CB THR B 87 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 1634 not shown) Planarity restraints: 1761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 73 " -0.080 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO A 74 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 258 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.14e+00 pdb=" C ASP B 258 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP B 258 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN B 259 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 293 " -0.043 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO D 294 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 294 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 294 " -0.037 5.00e-02 4.00e+02 ... (remaining 1758 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 110 2.61 - 3.18: 8800 3.18 - 3.75: 16027 3.75 - 4.33: 20680 4.33 - 4.90: 34526 Nonbonded interactions: 80143 Sorted by model distance: nonbonded pdb=" OD1 ASP D 86 " pdb=" OG SER D 290 " model vdw 2.034 3.040 nonbonded pdb=" OD1 ASP A 86 " pdb=" OG SER A 290 " model vdw 2.095 3.040 nonbonded pdb=" OG SER N 52 " pdb=" OG SER N 57 " model vdw 2.180 3.040 nonbonded pdb=" ND2 ASN B 88 " pdb=" OE1 GLN C 19 " model vdw 2.189 3.120 nonbonded pdb=" OD1 ASP A 271 " pdb=" OG SER A 274 " model vdw 2.197 3.040 ... (remaining 80138 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 143 or (resid 144 and (name N or name CA or nam \ e C or name O or name CB )) or resid 145 through 312)) selection = (chain 'D' and (resid 35 through 232 or resid 241 through 312)) } 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: 1.410 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: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.330 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 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 : 0.004 0.083 10266 Z= 0.174 Angle : 0.685 12.097 13967 Z= 0.353 Chirality : 0.042 0.180 1637 Planarity : 0.005 0.119 1761 Dihedral : 15.516 79.607 3617 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.75 % Allowed : 24.06 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.99 (0.24), residues: 1292 helix: 1.67 (0.21), residues: 610 sheet: 0.69 (0.34), residues: 233 loop : -0.74 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 281 HIS 0.007 0.001 HIS B 91 PHE 0.020 0.002 PHE A 97 TYR 0.014 0.001 TYR D 266 ARG 0.006 0.000 ARG C 317 Details of bonding type rmsd hydrogen bonds : bond 0.14119 ( 577) hydrogen bonds : angle 5.32395 ( 1683) SS BOND : bond 0.00116 ( 4) SS BOND : angle 1.36415 ( 8) covalent geometry : bond 0.00360 (10262) covalent geometry : angle 0.68411 (13959) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 309 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.7890 (t) cc_final: 0.7581 (p) REVERT: B 4 LEU cc_start: 0.7395 (tp) cc_final: 0.7119 (tt) REVERT: B 19 ARG cc_start: 0.7756 (ttp-170) cc_final: 0.7526 (ttp80) REVERT: B 25 CYS cc_start: 0.7804 (m) cc_final: 0.7508 (m) REVERT: B 50 THR cc_start: 0.8365 (m) cc_final: 0.7916 (t) REVERT: B 188 MET cc_start: 0.7986 (mmm) cc_final: 0.7458 (mmm) REVERT: B 217 MET cc_start: 0.7272 (ptt) cc_final: 0.7061 (ptt) REVERT: B 230 ASN cc_start: 0.8254 (m-40) cc_final: 0.7911 (m110) REVERT: B 246 ASP cc_start: 0.7833 (m-30) cc_final: 0.7549 (m-30) REVERT: B 253 PHE cc_start: 0.8465 (m-80) cc_final: 0.8198 (m-80) REVERT: B 259 GLN cc_start: 0.7795 (pt0) cc_final: 0.7547 (pt0) REVERT: B 262 MET cc_start: 0.7810 (tpt) cc_final: 0.7480 (mtp) REVERT: B 291 ASP cc_start: 0.8173 (p0) cc_final: 0.7735 (p0) REVERT: B 296 VAL cc_start: 0.8153 (t) cc_final: 0.7924 (p) REVERT: B 297 TRP cc_start: 0.8401 (m100) cc_final: 0.8108 (m100) REVERT: B 323 ASP cc_start: 0.8356 (p0) cc_final: 0.7537 (p0) REVERT: C 228 ARG cc_start: 0.7872 (mtm180) cc_final: 0.7342 (mtp180) REVERT: C 230 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7414 (mt-10) REVERT: C 242 THR cc_start: 0.8684 (m) cc_final: 0.8465 (t) REVERT: C 381 ASP cc_start: 0.7702 (t0) cc_final: 0.7499 (t0) REVERT: C 389 ARG cc_start: 0.7612 (ttt-90) cc_final: 0.7362 (ttt-90) REVERT: D 48 CYS cc_start: 0.5783 (t) cc_final: 0.5451 (t) REVERT: D 97 PHE cc_start: 0.6446 (t80) cc_final: 0.6045 (t80) REVERT: D 130 ILE cc_start: 0.8489 (mt) cc_final: 0.8126 (tt) REVERT: G 29 LYS cc_start: 0.8218 (mmmt) cc_final: 0.7538 (mmmt) REVERT: N 25 SER cc_start: 0.8285 (p) cc_final: 0.8012 (m) REVERT: N 35 ASN cc_start: 0.7517 (m-40) cc_final: 0.7283 (m-40) REVERT: N 38 ARG cc_start: 0.7572 (ptt90) cc_final: 0.6587 (ttp-170) REVERT: N 87 LYS cc_start: 0.7963 (mttt) cc_final: 0.7650 (mtmm) REVERT: N 118 ARG cc_start: 0.8736 (ttm110) cc_final: 0.8495 (ttm170) REVERT: N 120 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7505 (mm-40) outliers start: 8 outliers final: 4 residues processed: 310 average time/residue: 0.2942 time to fit residues: 122.0746 Evaluate side-chains 267 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 263 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 153 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 0.0030 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 0.0770 chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.5552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 119 ASN B 176 GLN B 239 ASN B 295 ASN C 23 ASN ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.159161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.138070 restraints weight = 14992.335| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.51 r_work: 0.3684 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10266 Z= 0.145 Angle : 0.621 10.336 13967 Z= 0.316 Chirality : 0.042 0.168 1637 Planarity : 0.005 0.074 1761 Dihedral : 4.919 51.073 1423 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.93 % Allowed : 20.32 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.21 (0.24), residues: 1292 helix: 2.00 (0.20), residues: 616 sheet: 0.71 (0.35), residues: 219 loop : -0.82 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 161 HIS 0.005 0.001 HIS C 357 PHE 0.018 0.002 PHE D 256 TYR 0.014 0.001 TYR N 32 ARG 0.006 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 577) hydrogen bonds : angle 4.38189 ( 1683) SS BOND : bond 0.00642 ( 4) SS BOND : angle 0.85071 ( 8) covalent geometry : bond 0.00315 (10262) covalent geometry : angle 0.62065 (13959) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 281 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8124 (t) cc_final: 0.7886 (p) REVERT: A 291 MET cc_start: 0.7338 (ttm) cc_final: 0.7038 (ttm) REVERT: B 18 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7380 (tt) REVERT: B 19 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.7764 (ttp80) REVERT: B 25 CYS cc_start: 0.7969 (m) cc_final: 0.7485 (t) REVERT: B 89 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7626 (mttt) REVERT: B 119 ASN cc_start: 0.7893 (m-40) cc_final: 0.7537 (m-40) REVERT: B 137 ARG cc_start: 0.7556 (tpp80) cc_final: 0.7035 (tpp80) REVERT: B 177 THR cc_start: 0.7893 (m) cc_final: 0.7596 (p) REVERT: B 188 MET cc_start: 0.7975 (mmm) cc_final: 0.7403 (mmm) REVERT: B 217 MET cc_start: 0.7844 (ptt) cc_final: 0.7608 (ptt) REVERT: B 230 ASN cc_start: 0.8222 (m-40) cc_final: 0.7915 (m110) REVERT: B 246 ASP cc_start: 0.7898 (m-30) cc_final: 0.7578 (m-30) REVERT: B 253 PHE cc_start: 0.8392 (m-80) cc_final: 0.8166 (m-80) REVERT: B 262 MET cc_start: 0.7843 (tpt) cc_final: 0.7480 (mmm) REVERT: B 273 ILE cc_start: 0.8291 (mp) cc_final: 0.8063 (mt) REVERT: B 291 ASP cc_start: 0.8311 (p0) cc_final: 0.7924 (p0) REVERT: B 323 ASP cc_start: 0.8515 (p0) cc_final: 0.7866 (p0) REVERT: C 21 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6609 (tm-30) REVERT: C 38 ARG cc_start: 0.7449 (ttm-80) cc_final: 0.7144 (ttm-80) REVERT: C 218 ASN cc_start: 0.7668 (m-40) cc_final: 0.7358 (m-40) REVERT: C 228 ARG cc_start: 0.8331 (mtm180) cc_final: 0.7942 (mtp-110) REVERT: C 230 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7392 (mt-10) REVERT: C 242 THR cc_start: 0.8752 (m) cc_final: 0.8476 (t) REVERT: C 279 ASN cc_start: 0.8392 (t0) cc_final: 0.8092 (t0) REVERT: C 342 ARG cc_start: 0.7848 (ttp-170) cc_final: 0.7548 (ttt-90) REVERT: D 79 VAL cc_start: 0.8075 (t) cc_final: 0.7849 (t) REVERT: D 292 ILE cc_start: 0.7873 (tt) cc_final: 0.7487 (tt) REVERT: N 35 ASN cc_start: 0.7927 (m-40) cc_final: 0.7667 (m110) REVERT: N 120 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7727 (mm-40) outliers start: 42 outliers final: 18 residues processed: 310 average time/residue: 0.2826 time to fit residues: 118.4020 Evaluate side-chains 291 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 270 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 61 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 ASN B 176 GLN B 239 ASN B 259 GLN C 23 ASN C 377 ASN ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 74 ASN N 123 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.154028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.132808 restraints weight = 15158.971| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.51 r_work: 0.3614 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10266 Z= 0.167 Angle : 0.615 11.581 13967 Z= 0.311 Chirality : 0.042 0.188 1637 Planarity : 0.004 0.065 1761 Dihedral : 4.601 46.185 1419 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.96 % Allowed : 22.66 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.27 (0.24), residues: 1292 helix: 2.10 (0.21), residues: 616 sheet: 0.61 (0.34), residues: 229 loop : -0.82 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS C 357 PHE 0.012 0.002 PHE A 97 TYR 0.012 0.001 TYR N 60 ARG 0.005 0.001 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04644 ( 577) hydrogen bonds : angle 4.32472 ( 1683) SS BOND : bond 0.01141 ( 4) SS BOND : angle 0.89337 ( 8) covalent geometry : bond 0.00371 (10262) covalent geometry : angle 0.61482 (13959) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 295 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7993 (tmm) cc_final: 0.7692 (tmm) REVERT: A 150 VAL cc_start: 0.8204 (t) cc_final: 0.7996 (p) REVERT: A 157 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8269 (mt) REVERT: A 225 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.7102 (mp10) REVERT: B 19 ARG cc_start: 0.8090 (ttp-170) cc_final: 0.7790 (ttp80) REVERT: B 25 CYS cc_start: 0.7964 (m) cc_final: 0.7740 (m) REVERT: B 50 THR cc_start: 0.8433 (m) cc_final: 0.8192 (t) REVERT: B 119 ASN cc_start: 0.8066 (m-40) cc_final: 0.7785 (m110) REVERT: B 150 ARG cc_start: 0.8144 (mmt-90) cc_final: 0.7799 (mmt-90) REVERT: B 188 MET cc_start: 0.7944 (mmm) cc_final: 0.7361 (mmm) REVERT: B 217 MET cc_start: 0.7871 (ptt) cc_final: 0.7665 (ptt) REVERT: B 230 ASN cc_start: 0.8194 (m-40) cc_final: 0.7901 (m110) REVERT: B 239 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8215 (m-40) REVERT: B 246 ASP cc_start: 0.7947 (m-30) cc_final: 0.7548 (m-30) REVERT: B 256 ARG cc_start: 0.6780 (mpp-170) cc_final: 0.6529 (mpp-170) REVERT: B 262 MET cc_start: 0.7935 (tpt) cc_final: 0.7540 (mmm) REVERT: B 297 TRP cc_start: 0.8479 (m100) cc_final: 0.8060 (m100) REVERT: C 20 ARG cc_start: 0.7810 (mtt-85) cc_final: 0.7506 (mtt-85) REVERT: C 24 LYS cc_start: 0.7912 (mtpp) cc_final: 0.7708 (mtpp) REVERT: C 31 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7959 (mm-40) REVERT: C 34 LYS cc_start: 0.8298 (tttp) cc_final: 0.7786 (tttp) REVERT: C 38 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7315 (ttm-80) REVERT: C 218 ASN cc_start: 0.7845 (m-40) cc_final: 0.7422 (m-40) REVERT: C 228 ARG cc_start: 0.8287 (mtm180) cc_final: 0.7894 (mtp-110) REVERT: C 279 ASN cc_start: 0.8466 (t0) cc_final: 0.8175 (t0) REVERT: C 289 LEU cc_start: 0.7869 (tp) cc_final: 0.7614 (tp) REVERT: C 342 ARG cc_start: 0.7971 (ttp-170) cc_final: 0.7661 (ttt-90) REVERT: C 376 PHE cc_start: 0.8093 (t80) cc_final: 0.7658 (t80) REVERT: C 381 ASP cc_start: 0.7313 (t0) cc_final: 0.7070 (t0) REVERT: D 289 ASN cc_start: 0.7486 (OUTLIER) cc_final: 0.6871 (t0) REVERT: N 35 ASN cc_start: 0.8138 (m-40) cc_final: 0.7844 (m110) REVERT: N 38 ARG cc_start: 0.7761 (ptt90) cc_final: 0.6969 (ptt90) REVERT: N 120 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7684 (mm-40) outliers start: 53 outliers final: 30 residues processed: 323 average time/residue: 0.2687 time to fit residues: 116.2289 Evaluate side-chains 321 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 57 optimal weight: 2.9990 chunk 48 optimal weight: 0.0370 chunk 59 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 239 ASN C 377 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.154145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132774 restraints weight = 14971.037| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.50 r_work: 0.3609 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10266 Z= 0.138 Angle : 0.605 10.271 13967 Z= 0.304 Chirality : 0.040 0.151 1637 Planarity : 0.004 0.070 1761 Dihedral : 4.269 21.541 1415 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.49 % Allowed : 24.72 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.25 (0.24), residues: 1292 helix: 2.09 (0.21), residues: 617 sheet: 0.59 (0.34), residues: 222 loop : -0.83 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 234 HIS 0.004 0.001 HIS C 357 PHE 0.015 0.001 PHE C 315 TYR 0.010 0.001 TYR N 60 ARG 0.008 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 577) hydrogen bonds : angle 4.22919 ( 1683) SS BOND : bond 0.00437 ( 4) SS BOND : angle 0.46516 ( 8) covalent geometry : bond 0.00308 (10262) covalent geometry : angle 0.60508 (13959) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 304 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8210 (t) cc_final: 0.8007 (p) REVERT: A 157 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8258 (mt) REVERT: B 19 ARG cc_start: 0.8109 (ttp-170) cc_final: 0.7577 (ttp80) REVERT: B 49 ARG cc_start: 0.8541 (mmt-90) cc_final: 0.8104 (mpt180) REVERT: B 126 LEU cc_start: 0.7516 (mt) cc_final: 0.7303 (mt) REVERT: B 137 ARG cc_start: 0.7899 (tpp80) cc_final: 0.7325 (tpp80) REVERT: B 150 ARG cc_start: 0.8124 (mmt-90) cc_final: 0.7763 (mmt-90) REVERT: B 188 MET cc_start: 0.7914 (mmm) cc_final: 0.7310 (mmm) REVERT: B 217 MET cc_start: 0.7981 (ptt) cc_final: 0.7741 (ptt) REVERT: B 222 PHE cc_start: 0.8680 (m-80) cc_final: 0.8448 (m-80) REVERT: B 230 ASN cc_start: 0.8204 (m-40) cc_final: 0.7904 (m110) REVERT: B 246 ASP cc_start: 0.7959 (m-30) cc_final: 0.7568 (m-30) REVERT: B 253 PHE cc_start: 0.8605 (m-80) cc_final: 0.8317 (m-80) REVERT: B 262 MET cc_start: 0.7881 (tpt) cc_final: 0.7457 (mmm) REVERT: B 291 ASP cc_start: 0.8218 (p0) cc_final: 0.7933 (p0) REVERT: B 297 TRP cc_start: 0.8433 (m100) cc_final: 0.8101 (m100) REVERT: C 21 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: C 24 LYS cc_start: 0.7837 (mtpp) cc_final: 0.7618 (mtpp) REVERT: C 31 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7879 (mm-40) REVERT: C 34 LYS cc_start: 0.8288 (tttp) cc_final: 0.7674 (tttp) REVERT: C 38 ARG cc_start: 0.7753 (ttm-80) cc_final: 0.7240 (ttm-80) REVERT: C 218 ASN cc_start: 0.7834 (m-40) cc_final: 0.7402 (m-40) REVERT: C 219 PHE cc_start: 0.8033 (m-10) cc_final: 0.7681 (m-10) REVERT: C 274 ASP cc_start: 0.8045 (t0) cc_final: 0.7823 (t0) REVERT: C 279 ASN cc_start: 0.8441 (t0) cc_final: 0.8184 (t0) REVERT: C 289 LEU cc_start: 0.7797 (tp) cc_final: 0.7538 (tp) REVERT: C 342 ARG cc_start: 0.7917 (ttp-170) cc_final: 0.7618 (ttt-90) REVERT: C 360 TYR cc_start: 0.8176 (m-80) cc_final: 0.7958 (m-80) REVERT: C 376 PHE cc_start: 0.8083 (t80) cc_final: 0.7691 (t80) REVERT: D 82 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6955 (tp) REVERT: N 35 ASN cc_start: 0.8110 (m-40) cc_final: 0.7819 (m110) REVERT: N 39 GLN cc_start: 0.8242 (tp40) cc_final: 0.7964 (tt0) REVERT: N 120 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7490 (mm-40) outliers start: 48 outliers final: 33 residues processed: 329 average time/residue: 0.2623 time to fit residues: 117.0123 Evaluate side-chains 327 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 291 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 239 ASN C 377 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.153004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.131532 restraints weight = 14826.078| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.49 r_work: 0.3581 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10266 Z= 0.161 Angle : 0.612 9.763 13967 Z= 0.309 Chirality : 0.041 0.193 1637 Planarity : 0.004 0.070 1761 Dihedral : 4.323 21.865 1415 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.96 % Allowed : 24.16 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.10 (0.24), residues: 1292 helix: 1.99 (0.21), residues: 621 sheet: 0.45 (0.34), residues: 223 loop : -0.93 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 281 HIS 0.007 0.001 HIS B 54 PHE 0.012 0.002 PHE B 234 TYR 0.011 0.001 TYR N 60 ARG 0.007 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 577) hydrogen bonds : angle 4.19300 ( 1683) SS BOND : bond 0.00284 ( 4) SS BOND : angle 0.48792 ( 8) covalent geometry : bond 0.00365 (10262) covalent geometry : angle 0.61173 (13959) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 301 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8538 (mt) cc_final: 0.8304 (mp) REVERT: A 157 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8324 (mt) REVERT: A 225 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: B 19 ARG cc_start: 0.8174 (ttp-170) cc_final: 0.7633 (ttp80) REVERT: B 150 ARG cc_start: 0.8123 (mmt-90) cc_final: 0.7813 (mmt-90) REVERT: B 153 ASP cc_start: 0.8268 (p0) cc_final: 0.7971 (p0) REVERT: B 188 MET cc_start: 0.7914 (mmm) cc_final: 0.7275 (mmm) REVERT: B 217 MET cc_start: 0.7968 (ptt) cc_final: 0.7750 (ptt) REVERT: B 222 PHE cc_start: 0.8704 (m-80) cc_final: 0.8496 (m-80) REVERT: B 230 ASN cc_start: 0.8227 (m-40) cc_final: 0.7893 (m110) REVERT: B 246 ASP cc_start: 0.8005 (m-30) cc_final: 0.7610 (m-30) REVERT: B 262 MET cc_start: 0.7875 (tpt) cc_final: 0.7431 (mmm) REVERT: C 21 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6707 (tm-30) REVERT: C 31 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7842 (mm-40) REVERT: C 34 LYS cc_start: 0.8313 (tttp) cc_final: 0.7680 (tttp) REVERT: C 38 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7336 (ttm-80) REVERT: C 60 MET cc_start: 0.4511 (OUTLIER) cc_final: 0.3864 (ttm) REVERT: C 218 ASN cc_start: 0.7846 (m-40) cc_final: 0.7500 (m-40) REVERT: C 219 PHE cc_start: 0.8126 (m-10) cc_final: 0.7671 (m-80) REVERT: C 274 ASP cc_start: 0.8047 (t0) cc_final: 0.7817 (t0) REVERT: C 279 ASN cc_start: 0.8481 (t0) cc_final: 0.8172 (t0) REVERT: C 289 LEU cc_start: 0.7821 (tp) cc_final: 0.7567 (tp) REVERT: C 342 ARG cc_start: 0.7960 (ttp-170) cc_final: 0.7651 (ttt-90) REVERT: C 376 PHE cc_start: 0.8181 (t80) cc_final: 0.7639 (t80) REVERT: C 378 ASP cc_start: 0.7872 (m-30) cc_final: 0.7433 (m-30) REVERT: D 82 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7101 (tp) REVERT: D 172 VAL cc_start: 0.7347 (t) cc_final: 0.7068 (p) REVERT: N 39 GLN cc_start: 0.8228 (tp40) cc_final: 0.7948 (tt0) REVERT: N 120 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7492 (mm-40) outliers start: 53 outliers final: 34 residues processed: 332 average time/residue: 0.2558 time to fit residues: 114.1055 Evaluate side-chains 333 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 294 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 67 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 75 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 239 ASN C 267 GLN C 377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.152953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.131080 restraints weight = 14961.635| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.50 r_work: 0.3586 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10266 Z= 0.143 Angle : 0.603 9.127 13967 Z= 0.305 Chirality : 0.041 0.153 1637 Planarity : 0.004 0.069 1761 Dihedral : 4.279 21.620 1415 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.24 % Allowed : 25.00 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.14 (0.24), residues: 1292 helix: 2.06 (0.21), residues: 618 sheet: 0.51 (0.34), residues: 221 loop : -0.97 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 281 HIS 0.003 0.001 HIS B 54 PHE 0.016 0.001 PHE D 101 TYR 0.011 0.001 TYR N 60 ARG 0.006 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 577) hydrogen bonds : angle 4.18610 ( 1683) SS BOND : bond 0.00201 ( 4) SS BOND : angle 0.40771 ( 8) covalent geometry : bond 0.00322 (10262) covalent geometry : angle 0.60287 (13959) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 292 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.8070 (tmm) cc_final: 0.7659 (tmm) REVERT: A 77 LEU cc_start: 0.8562 (mt) cc_final: 0.8299 (mp) REVERT: A 157 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8313 (mt) REVERT: A 225 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7226 (mp10) REVERT: B 19 ARG cc_start: 0.8185 (ttp-170) cc_final: 0.7618 (ttp80) REVERT: B 153 ASP cc_start: 0.8277 (p0) cc_final: 0.7978 (p0) REVERT: B 188 MET cc_start: 0.7859 (mmm) cc_final: 0.7309 (mmm) REVERT: B 217 MET cc_start: 0.8033 (ptt) cc_final: 0.7788 (ptt) REVERT: B 230 ASN cc_start: 0.8223 (m-40) cc_final: 0.7887 (m110) REVERT: B 246 ASP cc_start: 0.8018 (m-30) cc_final: 0.7611 (m-30) REVERT: B 253 PHE cc_start: 0.8621 (m-80) cc_final: 0.8364 (m-80) REVERT: B 262 MET cc_start: 0.7872 (tpt) cc_final: 0.7418 (mmm) REVERT: C 20 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7499 (mpt-90) REVERT: C 21 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6800 (tm-30) REVERT: C 29 GLN cc_start: 0.8302 (tp-100) cc_final: 0.7995 (tp-100) REVERT: C 31 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7786 (mm-40) REVERT: C 34 LYS cc_start: 0.8323 (tttp) cc_final: 0.7721 (tttp) REVERT: C 38 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7342 (ttm-80) REVERT: C 60 MET cc_start: 0.4503 (OUTLIER) cc_final: 0.3842 (ttm) REVERT: C 218 ASN cc_start: 0.7879 (m-40) cc_final: 0.7489 (m110) REVERT: C 219 PHE cc_start: 0.8159 (m-10) cc_final: 0.7678 (m-80) REVERT: C 274 ASP cc_start: 0.8075 (t0) cc_final: 0.7828 (t0) REVERT: C 279 ASN cc_start: 0.8464 (t0) cc_final: 0.8239 (t0) REVERT: C 289 LEU cc_start: 0.7794 (tp) cc_final: 0.7530 (tp) REVERT: C 342 ARG cc_start: 0.7975 (ttp-170) cc_final: 0.7661 (ttt-90) REVERT: C 376 PHE cc_start: 0.8156 (t80) cc_final: 0.7654 (t80) REVERT: C 378 ASP cc_start: 0.7856 (m-30) cc_final: 0.7390 (m-30) REVERT: D 82 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7158 (tp) REVERT: D 172 VAL cc_start: 0.7478 (t) cc_final: 0.7226 (p) REVERT: N 39 GLN cc_start: 0.8216 (tp40) cc_final: 0.7951 (tt0) REVERT: N 120 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7543 (mm-40) outliers start: 56 outliers final: 39 residues processed: 318 average time/residue: 0.2573 time to fit residues: 109.8440 Evaluate side-chains 332 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 287 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 119 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN C 377 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.155562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.134636 restraints weight = 15067.534| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.52 r_work: 0.3565 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10266 Z= 0.145 Angle : 0.607 9.674 13967 Z= 0.306 Chirality : 0.041 0.151 1637 Planarity : 0.004 0.068 1761 Dihedral : 4.254 22.135 1415 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.52 % Allowed : 24.34 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.17 (0.24), residues: 1292 helix: 2.08 (0.21), residues: 619 sheet: 0.49 (0.34), residues: 221 loop : -0.94 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS B 54 PHE 0.015 0.002 PHE C 208 TYR 0.010 0.001 TYR A 213 ARG 0.007 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 577) hydrogen bonds : angle 4.17029 ( 1683) SS BOND : bond 0.00247 ( 4) SS BOND : angle 0.40827 ( 8) covalent geometry : bond 0.00329 (10262) covalent geometry : angle 0.60752 (13959) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 288 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.8108 (tmm) cc_final: 0.7655 (tmm) REVERT: A 77 LEU cc_start: 0.8558 (mt) cc_final: 0.8291 (mp) REVERT: A 87 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7905 (tp) REVERT: A 127 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.8003 (mp) REVERT: A 157 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8318 (mt) REVERT: A 225 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7271 (mp10) REVERT: B 19 ARG cc_start: 0.8226 (ttp-170) cc_final: 0.7664 (ttp80) REVERT: B 150 ARG cc_start: 0.8140 (mmt-90) cc_final: 0.7822 (mmt-90) REVERT: B 188 MET cc_start: 0.7867 (mmm) cc_final: 0.7355 (mmm) REVERT: B 217 MET cc_start: 0.8039 (ptt) cc_final: 0.7773 (ptt) REVERT: B 230 ASN cc_start: 0.8206 (m-40) cc_final: 0.7854 (m110) REVERT: B 246 ASP cc_start: 0.7983 (m-30) cc_final: 0.7540 (m-30) REVERT: B 253 PHE cc_start: 0.8628 (m-80) cc_final: 0.8356 (m-80) REVERT: B 262 MET cc_start: 0.7923 (tpt) cc_final: 0.7437 (mmm) REVERT: C 20 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7418 (mpt-90) REVERT: C 31 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7760 (mm-40) REVERT: C 34 LYS cc_start: 0.8344 (tttp) cc_final: 0.7651 (tttp) REVERT: C 38 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7389 (ttm-80) REVERT: C 60 MET cc_start: 0.4560 (OUTLIER) cc_final: 0.3912 (ttm) REVERT: C 218 ASN cc_start: 0.7782 (m-40) cc_final: 0.7448 (m110) REVERT: C 219 PHE cc_start: 0.8119 (m-10) cc_final: 0.7664 (m-80) REVERT: C 274 ASP cc_start: 0.8050 (t0) cc_final: 0.7795 (t0) REVERT: C 279 ASN cc_start: 0.8456 (t0) cc_final: 0.8214 (t0) REVERT: C 289 LEU cc_start: 0.7790 (tp) cc_final: 0.7524 (tp) REVERT: C 342 ARG cc_start: 0.7965 (ttp-170) cc_final: 0.7644 (ttt-90) REVERT: C 376 PHE cc_start: 0.8182 (t80) cc_final: 0.7687 (t80) REVERT: C 378 ASP cc_start: 0.7896 (m-30) cc_final: 0.7434 (m-30) REVERT: D 82 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7187 (tp) REVERT: N 39 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: N 65 LYS cc_start: 0.8213 (tptp) cc_final: 0.7977 (tppp) REVERT: N 120 GLN cc_start: 0.8320 (mm-40) cc_final: 0.7535 (mm-40) outliers start: 59 outliers final: 40 residues processed: 318 average time/residue: 0.2847 time to fit residues: 121.6277 Evaluate side-chains 330 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 282 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 104 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN C 220 HIS C 377 ASN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.150282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.129081 restraints weight = 15001.288| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.48 r_work: 0.3551 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 10266 Z= 0.188 Angle : 0.652 11.610 13967 Z= 0.329 Chirality : 0.043 0.156 1637 Planarity : 0.004 0.068 1761 Dihedral : 4.377 22.151 1415 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.15 % Allowed : 24.81 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.00 (0.24), residues: 1292 helix: 1.91 (0.21), residues: 625 sheet: 0.31 (0.34), residues: 228 loop : -0.97 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 281 HIS 0.006 0.001 HIS B 54 PHE 0.016 0.002 PHE B 235 TYR 0.013 0.001 TYR N 60 ARG 0.007 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 577) hydrogen bonds : angle 4.26945 ( 1683) SS BOND : bond 0.00276 ( 4) SS BOND : angle 0.49758 ( 8) covalent geometry : bond 0.00427 (10262) covalent geometry : angle 0.65163 (13959) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 291 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.8115 (tmm) cc_final: 0.7639 (tmm) REVERT: A 77 LEU cc_start: 0.8576 (mt) cc_final: 0.8320 (mp) REVERT: A 87 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7909 (tp) REVERT: A 127 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8016 (mp) REVERT: A 157 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8344 (mt) REVERT: A 177 CYS cc_start: 0.5262 (t) cc_final: 0.4784 (t) REVERT: A 225 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7347 (mp10) REVERT: B 19 ARG cc_start: 0.8248 (ttp-170) cc_final: 0.7699 (ttp80) REVERT: B 50 THR cc_start: 0.8399 (m) cc_final: 0.8185 (t) REVERT: B 188 MET cc_start: 0.7870 (mmm) cc_final: 0.7445 (mmm) REVERT: B 230 ASN cc_start: 0.8241 (m-40) cc_final: 0.7891 (m110) REVERT: B 246 ASP cc_start: 0.8022 (m-30) cc_final: 0.7547 (m-30) REVERT: B 253 PHE cc_start: 0.8668 (m-80) cc_final: 0.8449 (m-80) REVERT: B 258 ASP cc_start: 0.7771 (t0) cc_final: 0.7169 (t0) REVERT: B 262 MET cc_start: 0.7956 (tpt) cc_final: 0.7505 (mmm) REVERT: C 20 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7366 (mpt-90) REVERT: C 29 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7712 (tp-100) REVERT: C 30 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7622 (mp) REVERT: C 33 ASP cc_start: 0.7535 (p0) cc_final: 0.7256 (p0) REVERT: C 34 LYS cc_start: 0.8362 (tttp) cc_final: 0.8020 (tttp) REVERT: C 38 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7526 (ttm-80) REVERT: C 60 MET cc_start: 0.4505 (OUTLIER) cc_final: 0.3851 (ttm) REVERT: C 218 ASN cc_start: 0.7744 (m-40) cc_final: 0.7380 (m-40) REVERT: C 219 PHE cc_start: 0.8086 (m-10) cc_final: 0.7659 (m-80) REVERT: C 274 ASP cc_start: 0.8043 (t0) cc_final: 0.7769 (t0) REVERT: C 289 LEU cc_start: 0.7859 (tp) cc_final: 0.7598 (tp) REVERT: C 307 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7350 (mmtm) REVERT: C 342 ARG cc_start: 0.7971 (ttp-170) cc_final: 0.7641 (ttt-90) REVERT: C 376 PHE cc_start: 0.8251 (t80) cc_final: 0.7724 (t80) REVERT: C 378 ASP cc_start: 0.7915 (m-30) cc_final: 0.7445 (m-30) REVERT: D 82 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7293 (tp) REVERT: D 183 THR cc_start: 0.7269 (t) cc_final: 0.6842 (p) REVERT: N 39 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: N 65 LYS cc_start: 0.8247 (tptp) cc_final: 0.7994 (tppp) REVERT: N 120 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7646 (mm-40) outliers start: 55 outliers final: 37 residues processed: 319 average time/residue: 0.2622 time to fit residues: 111.9706 Evaluate side-chains 331 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 285 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 57 optimal weight: 0.0570 chunk 118 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 76 optimal weight: 0.0970 chunk 1 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN C 19 GLN C 267 GLN C 377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.151825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.130537 restraints weight = 14985.562| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.49 r_work: 0.3576 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10266 Z= 0.137 Angle : 0.624 10.127 13967 Z= 0.316 Chirality : 0.042 0.152 1637 Planarity : 0.004 0.065 1761 Dihedral : 4.281 21.712 1415 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.21 % Allowed : 26.03 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1292 helix: 2.06 (0.21), residues: 619 sheet: 0.40 (0.35), residues: 211 loop : -0.91 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 281 HIS 0.006 0.001 HIS B 54 PHE 0.016 0.002 PHE C 208 TYR 0.011 0.001 TYR A 213 ARG 0.006 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 577) hydrogen bonds : angle 4.23524 ( 1683) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.32618 ( 8) covalent geometry : bond 0.00309 (10262) covalent geometry : angle 0.62399 (13959) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 287 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.8079 (tmm) cc_final: 0.7618 (tmm) REVERT: A 77 LEU cc_start: 0.8559 (mt) cc_final: 0.8303 (mp) REVERT: A 87 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7900 (tp) REVERT: A 127 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7994 (mp) REVERT: A 157 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8308 (mt) REVERT: A 225 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: A 280 TYR cc_start: 0.7813 (p90) cc_final: 0.7296 (p90) REVERT: B 19 ARG cc_start: 0.8247 (ttp-170) cc_final: 0.7749 (ttp80) REVERT: B 66 ASP cc_start: 0.7879 (p0) cc_final: 0.7674 (p0) REVERT: B 150 ARG cc_start: 0.8153 (mmt-90) cc_final: 0.7857 (mmt-90) REVERT: B 188 MET cc_start: 0.7872 (mmm) cc_final: 0.7248 (mmm) REVERT: B 230 ASN cc_start: 0.8198 (m-40) cc_final: 0.7860 (m110) REVERT: B 246 ASP cc_start: 0.7935 (m-30) cc_final: 0.7487 (m-30) REVERT: B 253 PHE cc_start: 0.8615 (m-80) cc_final: 0.8336 (m-80) REVERT: B 258 ASP cc_start: 0.7801 (t0) cc_final: 0.7217 (t0) REVERT: B 262 MET cc_start: 0.7954 (tpt) cc_final: 0.7477 (mmm) REVERT: C 20 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7353 (mpt-90) REVERT: C 29 GLN cc_start: 0.8277 (tp-100) cc_final: 0.7712 (tp-100) REVERT: C 33 ASP cc_start: 0.7551 (p0) cc_final: 0.7252 (p0) REVERT: C 34 LYS cc_start: 0.8352 (tttp) cc_final: 0.8000 (tttp) REVERT: C 38 ARG cc_start: 0.7888 (ttm-80) cc_final: 0.7501 (ttm-80) REVERT: C 60 MET cc_start: 0.4465 (OUTLIER) cc_final: 0.3794 (ttm) REVERT: C 218 ASN cc_start: 0.7711 (m-40) cc_final: 0.7386 (m-40) REVERT: C 219 PHE cc_start: 0.8111 (m-10) cc_final: 0.7708 (m-80) REVERT: C 274 ASP cc_start: 0.8030 (t0) cc_final: 0.7749 (t0) REVERT: C 289 LEU cc_start: 0.7745 (tp) cc_final: 0.7471 (tp) REVERT: C 307 LYS cc_start: 0.7683 (mmtt) cc_final: 0.7344 (mmtm) REVERT: C 342 ARG cc_start: 0.7973 (ttp-170) cc_final: 0.7640 (ttt-90) REVERT: C 376 PHE cc_start: 0.8200 (t80) cc_final: 0.7791 (t80) REVERT: C 378 ASP cc_start: 0.7910 (m-30) cc_final: 0.7444 (m-30) REVERT: D 82 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7303 (tp) REVERT: D 130 ILE cc_start: 0.8760 (mt) cc_final: 0.8444 (tt) REVERT: N 39 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: N 65 LYS cc_start: 0.8230 (tptp) cc_final: 0.7972 (tppp) REVERT: N 120 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7608 (mm-40) outliers start: 45 outliers final: 32 residues processed: 311 average time/residue: 0.2797 time to fit residues: 118.2087 Evaluate side-chains 321 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 281 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 96 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 57 optimal weight: 0.0870 chunk 118 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN C 236 GLN C 377 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.154741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.133403 restraints weight = 14964.134| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.53 r_work: 0.3563 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10266 Z= 0.143 Angle : 0.637 11.856 13967 Z= 0.320 Chirality : 0.042 0.178 1637 Planarity : 0.004 0.065 1761 Dihedral : 4.285 20.818 1415 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.03 % Allowed : 26.59 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.12 (0.24), residues: 1292 helix: 2.04 (0.21), residues: 619 sheet: 0.44 (0.35), residues: 209 loop : -0.91 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS B 54 PHE 0.015 0.002 PHE D 101 TYR 0.011 0.001 TYR A 213 ARG 0.006 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 577) hydrogen bonds : angle 4.24531 ( 1683) SS BOND : bond 0.00210 ( 4) SS BOND : angle 0.37758 ( 8) covalent geometry : bond 0.00327 (10262) covalent geometry : angle 0.63684 (13959) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 282 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.8108 (tmm) cc_final: 0.7631 (tmm) REVERT: A 77 LEU cc_start: 0.8560 (mt) cc_final: 0.8307 (mp) REVERT: A 87 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7915 (tp) REVERT: A 127 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7992 (mp) REVERT: A 157 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8321 (mt) REVERT: A 177 CYS cc_start: 0.5266 (t) cc_final: 0.4969 (t) REVERT: A 225 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7409 (mp10) REVERT: B 19 ARG cc_start: 0.8254 (ttp-170) cc_final: 0.7742 (ttp80) REVERT: B 188 MET cc_start: 0.7899 (mmm) cc_final: 0.7267 (mmm) REVERT: B 230 ASN cc_start: 0.8212 (m-40) cc_final: 0.7892 (m110) REVERT: B 246 ASP cc_start: 0.7924 (m-30) cc_final: 0.7511 (m-30) REVERT: B 253 PHE cc_start: 0.8612 (m-80) cc_final: 0.8315 (m-80) REVERT: B 258 ASP cc_start: 0.7833 (t0) cc_final: 0.7232 (t0) REVERT: B 262 MET cc_start: 0.7996 (tpt) cc_final: 0.7510 (mmm) REVERT: B 314 ARG cc_start: 0.8481 (mtp85) cc_final: 0.8198 (mmm160) REVERT: C 20 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7375 (mpt-90) REVERT: C 29 GLN cc_start: 0.8256 (tp-100) cc_final: 0.7688 (tp-100) REVERT: C 31 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7631 (mm-40) REVERT: C 33 ASP cc_start: 0.7528 (p0) cc_final: 0.7207 (p0) REVERT: C 34 LYS cc_start: 0.8324 (tttp) cc_final: 0.7635 (tttp) REVERT: C 38 ARG cc_start: 0.7790 (ttm-80) cc_final: 0.7228 (ttm-80) REVERT: C 60 MET cc_start: 0.4553 (OUTLIER) cc_final: 0.3906 (ttm) REVERT: C 218 ASN cc_start: 0.7711 (m-40) cc_final: 0.7374 (m110) REVERT: C 219 PHE cc_start: 0.8077 (m-10) cc_final: 0.7702 (m-80) REVERT: C 274 ASP cc_start: 0.8003 (t0) cc_final: 0.7764 (t0) REVERT: C 289 LEU cc_start: 0.7762 (tp) cc_final: 0.7490 (tp) REVERT: C 307 LYS cc_start: 0.7665 (mmtt) cc_final: 0.7329 (mmtm) REVERT: C 342 ARG cc_start: 0.7965 (ttp-170) cc_final: 0.7632 (ttt-90) REVERT: C 376 PHE cc_start: 0.8191 (t80) cc_final: 0.7796 (t80) REVERT: C 378 ASP cc_start: 0.7948 (m-30) cc_final: 0.7479 (m-30) REVERT: D 82 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7325 (tp) REVERT: D 130 ILE cc_start: 0.8778 (mt) cc_final: 0.8471 (tt) REVERT: D 183 THR cc_start: 0.7222 (t) cc_final: 0.6820 (p) REVERT: N 39 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: N 65 LYS cc_start: 0.8247 (tptp) cc_final: 0.7972 (tppp) REVERT: N 120 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7557 (mm-40) outliers start: 43 outliers final: 32 residues processed: 303 average time/residue: 0.2487 time to fit residues: 101.1754 Evaluate side-chains 321 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 281 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 90 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 0.0670 chunk 81 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 239 ASN C 236 GLN C 377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.155143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.133950 restraints weight = 15018.957| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.54 r_work: 0.3564 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10266 Z= 0.138 Angle : 0.631 11.685 13967 Z= 0.319 Chirality : 0.042 0.252 1637 Planarity : 0.004 0.064 1761 Dihedral : 4.278 20.653 1415 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.84 % Allowed : 27.34 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.11 (0.24), residues: 1292 helix: 2.00 (0.21), residues: 625 sheet: 0.45 (0.35), residues: 209 loop : -0.91 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 234 HIS 0.006 0.001 HIS B 54 PHE 0.016 0.002 PHE C 208 TYR 0.011 0.001 TYR A 213 ARG 0.007 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 577) hydrogen bonds : angle 4.22766 ( 1683) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.33219 ( 8) covalent geometry : bond 0.00313 (10262) covalent geometry : angle 0.63160 (13959) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6170.20 seconds wall clock time: 109 minutes 7.65 seconds (6547.65 seconds total)