Starting phenix.real_space_refine on Thu Feb 13 14:07:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vqx_32095/02_2025/7vqx_32095_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vqx_32095/02_2025/7vqx_32095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vqx_32095/02_2025/7vqx_32095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vqx_32095/02_2025/7vqx_32095.map" model { file = "/net/cci-nas-00/data/ceres_data/7vqx_32095/02_2025/7vqx_32095_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vqx_32095/02_2025/7vqx_32095_neut.cif" } resolution = 2.74 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= -0.001 sd= 0.077 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 60 5.16 5 C 5735 2.51 5 N 1566 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9049 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1962 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2598 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "L" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2877 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.26, per 1000 atoms: 0.58 Number of scatterers: 9049 At special positions: 0 Unit cell: (76.041, 101.745, 168.147, 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 60 16.00 O 1688 8.00 N 1566 7.00 C 5735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 38 " - pdb=" SG CYS R 61 " distance=2.04 Simple disulfide: pdb=" SG CYS R 52 " - pdb=" SG CYS R 93 " distance=2.03 Simple disulfide: pdb=" SG CYS R 75 " - pdb=" SG CYS R 109 " distance=2.03 Simple disulfide: pdb=" SG CYS R 202 " - pdb=" SG CYS R 271 " 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: 2.63 Conformation dependent library (CDL) restraints added in 1.1 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 41.8% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 4.657A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.500A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.568A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.748A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.936A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.714A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'L' and resid 2 through 27 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.740A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 43 removed outlier: 3.641A pdb=" N GLU R 30 " --> pdb=" O ARG R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 83 removed outlier: 5.183A pdb=" N ASN R 81 " --> pdb=" O VAL R 78 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR R 83 " --> pdb=" O SER R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 110 Processing helix chain 'R' and resid 115 through 117 No H-bonds generated for 'chain 'R' and resid 115 through 117' Processing helix chain 'R' and resid 118 through 151 removed outlier: 4.451A pdb=" N PHE R 122 " --> pdb=" O SER R 118 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR R 131 " --> pdb=" O LYS R 127 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR R 143 " --> pdb=" O MET R 139 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 155 Processing helix chain 'R' and resid 156 through 184 Processing helix chain 'R' and resid 195 through 233 removed outlier: 4.282A pdb=" N TRP R 199 " --> pdb=" O GLN R 195 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY R 224 " --> pdb=" O LEU R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 240 through 266 removed outlier: 4.245A pdb=" N LEU R 251 " --> pdb=" O ILE R 247 " (cutoff:3.500A) Proline residue: R 252 - end of helix Processing helix chain 'R' and resid 277 through 312 removed outlier: 3.779A pdb=" N TRP R 281 " --> pdb=" O HIS R 277 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE R 284 " --> pdb=" O PRO R 280 " (cutoff:3.500A) Proline residue: R 287 - end of helix removed outlier: 3.508A pdb=" N SER R 312 " --> pdb=" O GLN R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 323 through 338 Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 341 through 347 removed outlier: 3.911A pdb=" N VAL R 346 " --> pdb=" O MET R 342 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE R 347 " --> pdb=" O VAL R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 353 through 365 removed outlier: 3.791A pdb=" N CYS R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) Processing helix chain 'R' and resid 366 through 377 Processing helix chain 'R' and resid 379 through 393 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.365A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.382A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.629A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.780A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.545A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.874A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.576A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.872A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.574A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.009A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 70 through 74 451 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2955 1.34 - 1.46: 2043 1.46 - 1.58: 4162 1.58 - 1.70: 0 1.70 - 1.81: 79 Bond restraints: 9239 Sorted by residual: bond pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 1.808 1.761 0.047 3.30e-02 9.18e+02 2.01e+00 bond pdb=" C ARG N 98 " pdb=" N CYS N 99 " ideal model delta sigma weight residual 1.330 1.311 0.019 1.47e-02 4.63e+03 1.71e+00 bond pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.43e+00 bond pdb=" CB VAL N 110 " pdb=" CG1 VAL N 110 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CB ARG A 232 " pdb=" CG ARG A 232 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.14e+00 ... (remaining 9234 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 12154 1.38 - 2.76: 296 2.76 - 4.14: 50 4.14 - 5.52: 14 5.52 - 6.90: 2 Bond angle restraints: 12516 Sorted by residual: angle pdb=" C ILE B 58 " pdb=" N TYR B 59 " pdb=" CA TYR B 59 " ideal model delta sigma weight residual 122.11 117.23 4.88 1.64e+00 3.72e-01 8.84e+00 angle pdb=" C ILE R 286 " pdb=" CA ILE R 286 " pdb=" CB ILE R 286 " ideal model delta sigma weight residual 114.00 110.95 3.05 1.31e+00 5.83e-01 5.41e+00 angle pdb=" N PHE N 108 " pdb=" CA PHE N 108 " pdb=" C PHE N 108 " ideal model delta sigma weight residual 110.80 115.67 -4.87 2.13e+00 2.20e-01 5.24e+00 angle pdb=" C ARG R 285 " pdb=" N ILE R 286 " pdb=" CA ILE R 286 " ideal model delta sigma weight residual 120.33 122.08 -1.75 8.00e-01 1.56e+00 4.80e+00 angle pdb=" N GLY B 216 " pdb=" CA GLY B 216 " pdb=" C GLY B 216 " ideal model delta sigma weight residual 113.18 118.16 -4.98 2.37e+00 1.78e-01 4.42e+00 ... (remaining 12511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4952 17.38 - 34.77: 455 34.77 - 52.15: 77 52.15 - 69.53: 12 69.53 - 86.91: 16 Dihedral angle restraints: 5512 sinusoidal: 2172 harmonic: 3340 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 169.30 -76.30 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" CB CYS R 202 " pdb=" SG CYS R 202 " pdb=" SG CYS R 271 " pdb=" CB CYS R 271 " ideal model delta sinusoidal sigma weight residual 93.00 155.70 -62.70 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CB CYS R 38 " pdb=" SG CYS R 38 " pdb=" SG CYS R 61 " pdb=" CB CYS R 61 " ideal model delta sinusoidal sigma weight residual 93.00 137.10 -44.10 1 1.00e+01 1.00e-02 2.71e+01 ... (remaining 5509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 797 0.029 - 0.058: 384 0.058 - 0.087: 146 0.087 - 0.116: 61 0.116 - 0.145: 16 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 1401 not shown) Planarity restraints: 1594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO B 236 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 138 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C LEU R 138 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU R 138 " 0.012 2.00e-02 2.50e+03 pdb=" N MET R 139 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 131 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C THR R 131 " -0.032 2.00e-02 2.50e+03 pdb=" O THR R 131 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU R 132 " 0.011 2.00e-02 2.50e+03 ... (remaining 1591 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 125 2.66 - 3.22: 8325 3.22 - 3.78: 14306 3.78 - 4.34: 19806 4.34 - 4.90: 32728 Nonbonded interactions: 75290 Sorted by model distance: nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.094 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.147 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.172 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.238 3.040 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.259 3.120 ... (remaining 75285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.350 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 0.047 9239 Z= 0.233 Angle : 0.547 6.898 12516 Z= 0.298 Chirality : 0.042 0.145 1404 Planarity : 0.004 0.053 1594 Dihedral : 14.120 86.912 3334 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1130 helix: 1.55 (0.25), residues: 428 sheet: -0.19 (0.32), residues: 244 loop : -0.81 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 219 HIS 0.012 0.001 HIS A 357 PHE 0.018 0.001 PHE B 234 TYR 0.017 0.002 TYR B 59 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8197 (mt) cc_final: 0.7967 (mt) REVERT: A 299 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7186 (mm-30) REVERT: B 170 ASP cc_start: 0.7488 (t70) cc_final: 0.7106 (t70) REVERT: B 175 GLN cc_start: 0.7673 (mm110) cc_final: 0.7331 (mp10) REVERT: R 34 GLU cc_start: 0.6725 (tm-30) cc_final: 0.6507 (tm-30) REVERT: R 354 LYS cc_start: 0.6914 (mttp) cc_final: 0.6365 (ptmm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 1.5184 time to fit residues: 175.6726 Evaluate side-chains 94 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.0060 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 268 ASN N 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.185185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.127172 restraints weight = 8891.896| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.13 r_work: 0.3072 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9239 Z= 0.257 Angle : 0.558 6.711 12516 Z= 0.298 Chirality : 0.043 0.149 1404 Planarity : 0.004 0.052 1594 Dihedral : 4.390 17.885 1247 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.02 % Allowed : 8.32 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1130 helix: 1.99 (0.25), residues: 442 sheet: -0.11 (0.32), residues: 249 loop : -0.86 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 219 HIS 0.011 0.001 HIS A 357 PHE 0.016 0.001 PHE B 234 TYR 0.035 0.002 TYR R 130 ARG 0.003 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.998 Fit side-chains REVERT: A 296 LEU cc_start: 0.7730 (mt) cc_final: 0.7466 (mt) REVERT: A 299 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7523 (mm-30) REVERT: A 392 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: B 170 ASP cc_start: 0.8022 (t70) cc_final: 0.7515 (t70) REVERT: B 175 GLN cc_start: 0.7814 (mm110) cc_final: 0.7456 (mp10) REVERT: B 217 MET cc_start: 0.8160 (ptt) cc_final: 0.7646 (pp-130) REVERT: R 34 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6464 (tm-30) REVERT: R 354 LYS cc_start: 0.7009 (mttp) cc_final: 0.6337 (ptmm) REVERT: R 355 TYR cc_start: 0.7560 (m-80) cc_final: 0.7354 (m-80) outliers start: 10 outliers final: 6 residues processed: 119 average time/residue: 1.3746 time to fit residues: 174.0381 Evaluate side-chains 112 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 268 ASN R 155 HIS R 379 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.185323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.125583 restraints weight = 8997.730| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.10 r_work: 0.3061 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9239 Z= 0.272 Angle : 0.547 6.575 12516 Z= 0.293 Chirality : 0.043 0.148 1404 Planarity : 0.004 0.052 1594 Dihedral : 4.371 17.621 1247 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.54 % Allowed : 10.76 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1130 helix: 2.08 (0.25), residues: 443 sheet: -0.09 (0.33), residues: 249 loop : -0.88 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 219 HIS 0.010 0.001 HIS A 357 PHE 0.016 0.001 PHE B 151 TYR 0.028 0.002 TYR R 130 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.963 Fit side-chains REVERT: A 296 LEU cc_start: 0.7739 (mt) cc_final: 0.7488 (mt) REVERT: A 299 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7479 (mm-30) REVERT: A 392 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: B 170 ASP cc_start: 0.8021 (t70) cc_final: 0.7540 (t70) REVERT: B 175 GLN cc_start: 0.7817 (mm110) cc_final: 0.7450 (mp10) REVERT: B 217 MET cc_start: 0.8182 (ptt) cc_final: 0.7666 (pp-130) REVERT: R 354 LYS cc_start: 0.6802 (mttp) cc_final: 0.6089 (ptmm) outliers start: 25 outliers final: 15 residues processed: 117 average time/residue: 1.2852 time to fit residues: 160.5302 Evaluate side-chains 115 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 332 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 107 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.185163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127163 restraints weight = 8966.703| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.87 r_work: 0.3118 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9239 Z= 0.170 Angle : 0.490 6.541 12516 Z= 0.264 Chirality : 0.041 0.146 1404 Planarity : 0.003 0.052 1594 Dihedral : 4.197 17.800 1247 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.13 % Allowed : 13.30 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1130 helix: 2.34 (0.25), residues: 440 sheet: -0.15 (0.33), residues: 251 loop : -0.77 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 219 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.022 0.001 TYR R 130 ARG 0.002 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.046 Fit side-chains REVERT: A 296 LEU cc_start: 0.7731 (mt) cc_final: 0.7454 (mt) REVERT: A 299 GLU cc_start: 0.7561 (mm-30) cc_final: 0.6804 (mm-30) REVERT: A 392 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: B 170 ASP cc_start: 0.7944 (t70) cc_final: 0.7470 (t70) REVERT: B 175 GLN cc_start: 0.7737 (mm110) cc_final: 0.7358 (mp10) REVERT: B 217 MET cc_start: 0.8110 (ptt) cc_final: 0.7616 (pp-130) REVERT: N 35 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7331 (p0) REVERT: N 53 GLN cc_start: 0.8137 (mp10) cc_final: 0.7830 (mp10) REVERT: R 185 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7597 (p) REVERT: R 267 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7475 (pt0) REVERT: R 354 LYS cc_start: 0.6766 (mttp) cc_final: 0.6064 (ptmm) REVERT: R 381 GLU cc_start: 0.7573 (tt0) cc_final: 0.7262 (pt0) outliers start: 21 outliers final: 11 residues processed: 113 average time/residue: 1.3142 time to fit residues: 158.1254 Evaluate side-chains 112 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 267 GLU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 0.5980 chunk 59 optimal weight: 0.0770 chunk 16 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.184959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.126397 restraints weight = 9017.775| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.91 r_work: 0.3121 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9239 Z= 0.178 Angle : 0.490 6.391 12516 Z= 0.263 Chirality : 0.041 0.145 1404 Planarity : 0.004 0.051 1594 Dihedral : 4.083 15.900 1247 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.34 % Allowed : 14.21 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1130 helix: 2.42 (0.25), residues: 440 sheet: -0.15 (0.32), residues: 251 loop : -0.75 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 219 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.022 0.001 TYR R 130 ARG 0.001 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7631 (mt) cc_final: 0.7381 (mt) REVERT: A 299 GLU cc_start: 0.7597 (mm-30) cc_final: 0.6872 (mm-30) REVERT: A 392 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: B 170 ASP cc_start: 0.8027 (t70) cc_final: 0.7525 (t70) REVERT: B 175 GLN cc_start: 0.7717 (mm110) cc_final: 0.7339 (mp10) REVERT: N 34 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8406 (mmm) REVERT: N 35 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7296 (p0) REVERT: N 53 GLN cc_start: 0.8092 (mp10) cc_final: 0.7781 (mp10) REVERT: R 35 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7178 (mp0) REVERT: R 185 SER cc_start: 0.8051 (OUTLIER) cc_final: 0.7550 (p) REVERT: R 267 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: R 381 GLU cc_start: 0.7596 (tt0) cc_final: 0.7341 (pt0) outliers start: 23 outliers final: 14 residues processed: 116 average time/residue: 1.3246 time to fit residues: 163.9229 Evaluate side-chains 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 267 GLU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.185565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127179 restraints weight = 8884.241| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.91 r_work: 0.3116 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9239 Z= 0.162 Angle : 0.480 7.314 12516 Z= 0.258 Chirality : 0.040 0.144 1404 Planarity : 0.003 0.053 1594 Dihedral : 4.014 15.551 1247 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.54 % Allowed : 14.62 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1130 helix: 2.47 (0.25), residues: 440 sheet: -0.14 (0.32), residues: 251 loop : -0.72 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 219 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.021 0.001 TYR R 130 ARG 0.002 0.000 ARG R 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7634 (mt) cc_final: 0.7387 (mt) REVERT: A 299 GLU cc_start: 0.7528 (mm-30) cc_final: 0.6783 (mm-30) REVERT: A 392 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: B 175 GLN cc_start: 0.7545 (mm110) cc_final: 0.7162 (mp10) REVERT: B 277 SER cc_start: 0.8978 (t) cc_final: 0.8692 (p) REVERT: N 34 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8417 (mmm) REVERT: N 35 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7350 (p0) REVERT: N 53 GLN cc_start: 0.7977 (mp10) cc_final: 0.7662 (mp10) REVERT: N 80 TYR cc_start: 0.8141 (m-80) cc_final: 0.7862 (m-80) REVERT: R 35 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7271 (mp0) REVERT: R 185 SER cc_start: 0.8070 (OUTLIER) cc_final: 0.7562 (p) REVERT: R 267 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7465 (pt0) REVERT: R 354 LYS cc_start: 0.6933 (mttp) cc_final: 0.6122 (ptmm) REVERT: R 381 GLU cc_start: 0.7593 (tt0) cc_final: 0.7326 (pt0) outliers start: 25 outliers final: 9 residues processed: 117 average time/residue: 1.2656 time to fit residues: 158.5532 Evaluate side-chains 112 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 267 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.185195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.126490 restraints weight = 9010.304| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.93 r_work: 0.3106 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9239 Z= 0.186 Angle : 0.496 7.497 12516 Z= 0.266 Chirality : 0.040 0.145 1404 Planarity : 0.004 0.055 1594 Dihedral : 4.080 22.347 1247 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.83 % Allowed : 15.53 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1130 helix: 2.50 (0.25), residues: 440 sheet: -0.10 (0.33), residues: 251 loop : -0.74 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 219 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.022 0.001 TYR R 130 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7643 (mt) cc_final: 0.7389 (mt) REVERT: A 299 GLU cc_start: 0.7560 (mm-30) cc_final: 0.6818 (mm-30) REVERT: A 392 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: B 175 GLN cc_start: 0.7644 (mm110) cc_final: 0.7268 (mp10) REVERT: N 34 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8444 (mmm) REVERT: N 35 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7285 (p0) REVERT: N 53 GLN cc_start: 0.7964 (mp10) cc_final: 0.7729 (mp10) REVERT: N 80 TYR cc_start: 0.8206 (m-80) cc_final: 0.7956 (m-80) REVERT: R 35 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7484 (mp0) REVERT: R 185 SER cc_start: 0.8003 (OUTLIER) cc_final: 0.7513 (p) REVERT: R 267 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7486 (pt0) REVERT: R 381 GLU cc_start: 0.7577 (tt0) cc_final: 0.7321 (pt0) outliers start: 18 outliers final: 11 residues processed: 116 average time/residue: 1.2745 time to fit residues: 157.9028 Evaluate side-chains 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 267 GLU Chi-restraints excluded: chain R residue 332 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 61 optimal weight: 0.0980 chunk 78 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 104 optimal weight: 0.0980 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.188941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131428 restraints weight = 9049.700| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.93 r_work: 0.3135 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9239 Z= 0.149 Angle : 0.477 7.083 12516 Z= 0.257 Chirality : 0.040 0.154 1404 Planarity : 0.003 0.055 1594 Dihedral : 3.984 21.158 1247 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.73 % Allowed : 15.94 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1130 helix: 2.56 (0.25), residues: 439 sheet: -0.05 (0.33), residues: 249 loop : -0.73 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 219 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.021 0.001 TYR R 130 ARG 0.001 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7615 (mt) cc_final: 0.7381 (mt) REVERT: A 299 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6765 (mm-30) REVERT: A 392 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: B 175 GLN cc_start: 0.7559 (mm110) cc_final: 0.7186 (mp10) REVERT: N 34 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8468 (mmm) REVERT: N 35 ASN cc_start: 0.8226 (OUTLIER) cc_final: 0.7424 (p0) REVERT: N 53 GLN cc_start: 0.8022 (mp10) cc_final: 0.7802 (mp10) REVERT: N 80 TYR cc_start: 0.8210 (m-80) cc_final: 0.7949 (m-80) REVERT: R 35 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7318 (mp0) REVERT: R 185 SER cc_start: 0.8084 (OUTLIER) cc_final: 0.7586 (p) REVERT: R 267 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7369 (pt0) REVERT: R 354 LYS cc_start: 0.6963 (mttt) cc_final: 0.6146 (ptmm) outliers start: 17 outliers final: 9 residues processed: 118 average time/residue: 1.3242 time to fit residues: 166.6405 Evaluate side-chains 115 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 267 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.184284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.124313 restraints weight = 8910.695| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.04 r_work: 0.3095 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9239 Z= 0.185 Angle : 0.505 7.407 12516 Z= 0.269 Chirality : 0.041 0.147 1404 Planarity : 0.004 0.055 1594 Dihedral : 4.020 19.918 1247 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.83 % Allowed : 16.35 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.26), residues: 1130 helix: 2.49 (0.25), residues: 446 sheet: -0.09 (0.33), residues: 251 loop : -0.75 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 219 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.022 0.001 TYR R 130 ARG 0.004 0.000 ARG R 388 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7656 (mt) cc_final: 0.7419 (mt) REVERT: A 299 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6807 (mm-30) REVERT: A 392 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: B 175 GLN cc_start: 0.7716 (mm110) cc_final: 0.7347 (mp10) REVERT: N 34 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8481 (mmm) REVERT: N 35 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.7762 (p0) REVERT: N 53 GLN cc_start: 0.7979 (mp10) cc_final: 0.7744 (mp10) REVERT: R 34 GLU cc_start: 0.6928 (tm-30) cc_final: 0.6565 (tm-30) REVERT: R 35 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7416 (mm-30) REVERT: R 185 SER cc_start: 0.8005 (OUTLIER) cc_final: 0.7496 (p) REVERT: R 267 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: R 354 LYS cc_start: 0.6952 (mttt) cc_final: 0.6137 (ptmm) outliers start: 18 outliers final: 11 residues processed: 110 average time/residue: 1.3094 time to fit residues: 153.6001 Evaluate side-chains 113 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 267 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 0.6980 chunk 44 optimal weight: 0.0020 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 0.0020 chunk 89 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 104 optimal weight: 0.2980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.190476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.133658 restraints weight = 8996.412| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.91 r_work: 0.3155 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9239 Z= 0.133 Angle : 0.474 7.708 12516 Z= 0.253 Chirality : 0.039 0.139 1404 Planarity : 0.003 0.056 1594 Dihedral : 3.874 20.086 1247 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.83 % Allowed : 16.75 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1130 helix: 2.62 (0.25), residues: 440 sheet: 0.00 (0.33), residues: 250 loop : -0.74 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 219 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.020 0.001 TYR R 130 ARG 0.002 0.000 ARG R 388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7718 (mt) cc_final: 0.7488 (mt) REVERT: A 299 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6519 (mm-30) REVERT: A 392 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: B 175 GLN cc_start: 0.7513 (mm110) cc_final: 0.7136 (mp10) REVERT: N 53 GLN cc_start: 0.7917 (mp10) cc_final: 0.7684 (mp10) REVERT: N 80 TYR cc_start: 0.8155 (m-80) cc_final: 0.7900 (m-80) REVERT: R 34 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6550 (tm-30) REVERT: R 35 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7471 (mm-30) REVERT: R 185 SER cc_start: 0.8100 (OUTLIER) cc_final: 0.7639 (p) REVERT: R 267 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7240 (pt0) REVERT: R 354 LYS cc_start: 0.6912 (mttt) cc_final: 0.6120 (ptmm) outliers start: 18 outliers final: 12 residues processed: 108 average time/residue: 1.4478 time to fit residues: 166.8416 Evaluate side-chains 116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 267 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 1.9990 chunk 91 optimal weight: 0.0170 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.0060 chunk 93 optimal weight: 0.0770 chunk 55 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.187684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130174 restraints weight = 9076.781| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.89 r_work: 0.3160 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9239 Z= 0.137 Angle : 0.477 7.665 12516 Z= 0.253 Chirality : 0.039 0.141 1404 Planarity : 0.003 0.055 1594 Dihedral : 3.827 20.449 1247 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.62 % Allowed : 17.06 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1130 helix: 2.63 (0.25), residues: 440 sheet: 0.04 (0.33), residues: 249 loop : -0.72 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 219 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.020 0.001 TYR R 130 ARG 0.002 0.000 ARG R 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7674.27 seconds wall clock time: 135 minutes 57.67 seconds (8157.67 seconds total)