Starting phenix.real_space_refine on Thu Mar 13 16:44:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vqx_32095/03_2025/7vqx_32095_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vqx_32095/03_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_32095/03_2025/7vqx_32095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vqx_32095/03_2025/7vqx_32095.map" model { file = "/net/cci-nas-00/data/ceres_data/7vqx_32095/03_2025/7vqx_32095_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vqx_32095/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.54, per 1000 atoms: 0.61 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: 2.34 Conformation dependent library (CDL) restraints added in 1.2 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: 0.95 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: 2.56 Time building geometry restraints manager: 2.78 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.980 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.610 ------------------------------------------------------------------------------- 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 : 1.034 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: 1.4117 time to fit residues: 163.4660 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 : 1.032 ------------------------------------------------------------------------------- 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: 2.87 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: 0.7935 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 : 1.081 Fit side-chains REVERT: A 296 LEU cc_start: 0.7714 (mt) cc_final: 0.7450 (mt) REVERT: A 299 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7507 (mm-30) REVERT: A 392 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: B 170 ASP cc_start: 0.8018 (t70) cc_final: 0.7513 (t70) REVERT: B 175 GLN cc_start: 0.7816 (mm110) cc_final: 0.7459 (mp10) REVERT: B 217 MET cc_start: 0.8166 (ptt) cc_final: 0.7647 (pp-130) REVERT: R 34 GLU cc_start: 0.6747 (tm-30) cc_final: 0.6457 (tm-30) REVERT: R 354 LYS cc_start: 0.6995 (mttp) cc_final: 0.6323 (ptmm) REVERT: R 355 TYR cc_start: 0.7548 (m-80) cc_final: 0.7340 (m-80) outliers start: 10 outliers final: 6 residues processed: 119 average time/residue: 1.4453 time to fit residues: 183.0581 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 : 1.092 ------------------------------------------------------------------------------- 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: 2.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 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: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.185956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.127395 restraints weight = 8988.012| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.94 r_work: 0.3084 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9239 Z= 0.282 Angle : 0.553 6.598 12516 Z= 0.296 Chirality : 0.043 0.148 1404 Planarity : 0.004 0.052 1594 Dihedral : 4.389 17.840 1247 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.64 % Allowed : 10.76 % Favored : 86.60 % 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: 0.69 (0.26), residues: 1130 helix: 2.07 (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 0.002 PHE B 151 TYR 0.028 0.002 TYR R 130 ARG 0.003 0.000 ARG B 150 *********************** 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 133 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 1.464 Fit side-chains REVERT: A 296 LEU cc_start: 0.7675 (mt) cc_final: 0.7425 (mt) REVERT: A 299 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7449 (mm-30) REVERT: A 392 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: B 170 ASP cc_start: 0.7992 (t70) cc_final: 0.7471 (t70) REVERT: B 175 GLN cc_start: 0.7796 (mm110) cc_final: 0.7424 (mp10) REVERT: B 217 MET cc_start: 0.8144 (ptt) cc_final: 0.7618 (pp-130) REVERT: R 354 LYS cc_start: 0.6755 (mttp) cc_final: 0.6041 (ptmm) outliers start: 26 outliers final: 15 residues processed: 118 average time/residue: 1.4628 time to fit residues: 184.2384 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 : 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 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: 0.7980 chunk 111 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.186186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128107 restraints weight = 8913.326| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.92 r_work: 0.3079 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9239 Z= 0.241 Angle : 0.531 6.604 12516 Z= 0.284 Chirality : 0.042 0.148 1404 Planarity : 0.004 0.052 1594 Dihedral : 4.346 18.517 1247 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.74 % Allowed : 12.59 % Favored : 84.67 % 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: 0.81 (0.26), residues: 1130 helix: 2.24 (0.25), residues: 440 sheet: -0.09 (0.33), residues: 249 loop : -0.82 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 219 HIS 0.008 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.025 0.001 TYR R 130 ARG 0.003 0.000 ARG B 150 *********************** 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 129 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.908 Fit side-chains REVERT: A 296 LEU cc_start: 0.7755 (mt) cc_final: 0.7507 (mt) REVERT: A 299 GLU cc_start: 0.7651 (mm-30) cc_final: 0.6882 (mm-30) REVERT: A 392 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: B 170 ASP cc_start: 0.8031 (t70) cc_final: 0.7551 (t70) REVERT: B 175 GLN cc_start: 0.7811 (mm110) cc_final: 0.7445 (mp10) REVERT: B 217 MET cc_start: 0.8142 (ptt) cc_final: 0.7625 (pp-130) REVERT: N 35 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.7501 (p0) REVERT: N 53 GLN cc_start: 0.8210 (mp10) cc_final: 0.7935 (mp10) REVERT: R 267 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7559 (pt0) REVERT: R 354 LYS cc_start: 0.6833 (mttp) cc_final: 0.6104 (ptmm) outliers start: 27 outliers final: 16 residues processed: 117 average time/residue: 1.2168 time to fit residues: 152.3624 Evaluate side-chains 116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 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: 0.7980 chunk 82 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.183885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.125038 restraints weight = 9001.294| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.91 r_work: 0.3086 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9239 Z= 0.205 Angle : 0.506 6.546 12516 Z= 0.273 Chirality : 0.041 0.147 1404 Planarity : 0.004 0.052 1594 Dihedral : 4.211 16.729 1247 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.64 % Allowed : 14.11 % Favored : 83.25 % 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: 0.89 (0.26), residues: 1130 helix: 2.35 (0.25), residues: 440 sheet: -0.10 (0.32), residues: 249 loop : -0.80 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 219 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.023 0.001 TYR R 130 ARG 0.002 0.000 ARG B 150 *********************** 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 127 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7637 (mt) cc_final: 0.7389 (mt) REVERT: A 299 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6792 (mm-30) REVERT: A 392 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: B 170 ASP cc_start: 0.8058 (t70) cc_final: 0.7563 (t70) REVERT: B 175 GLN cc_start: 0.7726 (mm110) cc_final: 0.7346 (mp10) REVERT: N 34 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8496 (mmm) REVERT: N 53 GLN cc_start: 0.8146 (mp10) cc_final: 0.7809 (mp10) REVERT: R 35 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7240 (mp0) REVERT: R 267 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7511 (pt0) REVERT: R 354 LYS cc_start: 0.6809 (mttp) cc_final: 0.6082 (ptmm) REVERT: R 381 GLU cc_start: 0.7590 (tt0) cc_final: 0.7299 (pt0) outliers start: 26 outliers final: 17 residues processed: 113 average time/residue: 1.3045 time to fit residues: 157.1301 Evaluate side-chains 115 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 184 THR Chi-restraints excluded: chain B residue 186 ASP 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 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: 0.6980 chunk 4 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 106 optimal weight: 0.0770 chunk 66 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 91 optimal weight: 0.0570 chunk 48 optimal weight: 0.2980 chunk 44 optimal weight: 6.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.186316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128567 restraints weight = 8881.919| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.86 r_work: 0.3131 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9239 Z= 0.138 Angle : 0.469 6.572 12516 Z= 0.253 Chirality : 0.040 0.141 1404 Planarity : 0.003 0.052 1594 Dihedral : 3.982 15.632 1247 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.44 % Allowed : 14.72 % 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: 1.01 (0.26), residues: 1130 helix: 2.49 (0.25), residues: 440 sheet: -0.07 (0.33), residues: 247 loop : -0.75 (0.30), residues: 443 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 0.013 0.001 PHE A 212 TYR 0.020 0.001 TYR R 130 ARG 0.002 0.000 ARG N 72 *********************** 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 127 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7716 (mt) cc_final: 0.7474 (mt) REVERT: A 299 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6805 (mm-30) REVERT: A 392 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: B 175 GLN cc_start: 0.7536 (mm110) cc_final: 0.7160 (mp10) REVERT: N 35 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7338 (p0) REVERT: N 53 GLN cc_start: 0.7984 (mp10) cc_final: 0.7684 (mp10) REVERT: R 35 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7222 (mp0) REVERT: R 185 SER cc_start: 0.8061 (OUTLIER) cc_final: 0.7576 (p) REVERT: R 267 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7400 (pt0) REVERT: R 354 LYS cc_start: 0.6804 (mttp) cc_final: 0.6094 (ptmm) REVERT: R 381 GLU cc_start: 0.7577 (tt0) cc_final: 0.7373 (pt0) outliers start: 24 outliers final: 11 residues processed: 119 average time/residue: 1.2167 time to fit residues: 155.3428 Evaluate side-chains 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 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 378 LEU Chi-restraints excluded: chain R residue 380 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 35 optimal weight: 0.0040 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 104 optimal weight: 0.0970 chunk 34 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.185562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.126006 restraints weight = 9014.459| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.03 r_work: 0.3112 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 9239 Z= 0.146 Angle : 0.469 6.672 12516 Z= 0.253 Chirality : 0.040 0.143 1404 Planarity : 0.003 0.054 1594 Dihedral : 3.974 21.916 1247 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.62 % Allowed : 16.04 % 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: 1.08 (0.26), residues: 1130 helix: 2.57 (0.25), residues: 440 sheet: -0.05 (0.33), residues: 249 loop : -0.75 (0.30), residues: 441 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 0.012 0.001 PHE A 212 TYR 0.020 0.001 TYR R 130 ARG 0.004 0.000 ARG R 388 *********************** 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: 16 poor density : 107 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7616 (mt) cc_final: 0.7379 (mt) REVERT: A 299 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6779 (mm-30) REVERT: A 392 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: B 175 GLN cc_start: 0.7571 (mm110) cc_final: 0.7200 (mp10) REVERT: N 34 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8433 (mmm) REVERT: N 35 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7404 (p0) REVERT: N 53 GLN cc_start: 0.8002 (mp10) cc_final: 0.7750 (mp10) REVERT: N 80 TYR cc_start: 0.8159 (m-80) cc_final: 0.7913 (m-80) REVERT: R 34 GLU cc_start: 0.6920 (tm-30) cc_final: 0.6568 (tm-30) REVERT: R 35 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7342 (mm-30) REVERT: R 185 SER cc_start: 0.8028 (OUTLIER) cc_final: 0.7553 (p) REVERT: R 267 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7383 (pt0) outliers start: 16 outliers final: 10 residues processed: 116 average time/residue: 1.2801 time to fit residues: 158.5753 Evaluate side-chains 114 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 61 optimal weight: 0.0030 chunk 78 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.184003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.123959 restraints weight = 9087.302| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.05 r_work: 0.3103 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9239 Z= 0.177 Angle : 0.493 6.975 12516 Z= 0.264 Chirality : 0.040 0.145 1404 Planarity : 0.003 0.053 1594 Dihedral : 4.009 21.232 1247 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.93 % Allowed : 16.65 % 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: 1.10 (0.26), residues: 1130 helix: 2.60 (0.25), residues: 440 sheet: -0.06 (0.33), residues: 249 loop : -0.72 (0.30), residues: 441 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 0.012 0.001 PHE A 212 TYR 0.022 0.001 TYR R 130 ARG 0.004 0.000 ARG R 388 *********************** 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 125 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7695 (mt) cc_final: 0.7463 (mt) REVERT: A 299 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6818 (mm-30) REVERT: A 392 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: B 175 GLN cc_start: 0.7720 (mm110) cc_final: 0.7363 (mp10) REVERT: N 34 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8449 (mmm) REVERT: N 35 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.7430 (p0) REVERT: N 53 GLN cc_start: 0.7987 (mp10) cc_final: 0.7778 (mp10) REVERT: N 108 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7797 (t80) REVERT: R 34 GLU cc_start: 0.6950 (tm-30) cc_final: 0.6583 (tm-30) REVERT: R 35 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7421 (mm-30) REVERT: R 185 SER cc_start: 0.8058 (OUTLIER) cc_final: 0.7571 (p) REVERT: R 267 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: R 354 LYS cc_start: 0.7015 (mttt) cc_final: 0.6194 (ptmm) outliers start: 19 outliers final: 10 residues processed: 120 average time/residue: 1.2894 time to fit residues: 165.3264 Evaluate side-chains 123 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 108 PHE 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 380 SER 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: 2.9990 chunk 103 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 91 optimal weight: 0.3980 chunk 23 optimal weight: 0.0980 chunk 60 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.185604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.125999 restraints weight = 8904.856| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.04 r_work: 0.3130 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9239 Z= 0.144 Angle : 0.474 7.461 12516 Z= 0.253 Chirality : 0.040 0.142 1404 Planarity : 0.003 0.054 1594 Dihedral : 3.928 20.260 1247 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.73 % Allowed : 16.75 % Favored : 81.52 % 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: 1.10 (0.26), residues: 1130 helix: 2.54 (0.25), residues: 447 sheet: -0.02 (0.33), residues: 249 loop : -0.74 (0.31), residues: 434 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 0.012 0.001 PHE A 212 TYR 0.020 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 121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7728 (mt) cc_final: 0.7503 (mt) REVERT: A 299 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6552 (mm-30) REVERT: A 392 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: B 170 ASP cc_start: 0.8138 (t70) cc_final: 0.7672 (t70) REVERT: B 175 GLN cc_start: 0.7588 (mm110) cc_final: 0.7211 (mp10) REVERT: N 34 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8442 (mmm) REVERT: N 35 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7447 (p0) REVERT: N 53 GLN cc_start: 0.7954 (mp10) cc_final: 0.7744 (mp10) REVERT: R 34 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6558 (tm-30) REVERT: R 35 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7437 (mm-30) REVERT: R 185 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7567 (p) REVERT: R 267 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7382 (pt0) REVERT: R 354 LYS cc_start: 0.6998 (mttt) cc_final: 0.6182 (ptmm) outliers start: 17 outliers final: 10 residues processed: 115 average time/residue: 1.3174 time to fit residues: 161.5356 Evaluate side-chains 113 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 380 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 69 optimal weight: 0.0060 chunk 24 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 0.0030 chunk 62 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.4606 ------------------------------------------------------------------------------- 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 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.187457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129737 restraints weight = 9030.977| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.89 r_work: 0.3129 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9239 Z= 0.148 Angle : 0.486 7.718 12516 Z= 0.259 Chirality : 0.040 0.143 1404 Planarity : 0.003 0.053 1594 Dihedral : 3.890 19.739 1247 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.52 % Allowed : 17.36 % Favored : 81.12 % 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: 1.15 (0.26), residues: 1130 helix: 2.64 (0.25), residues: 441 sheet: -0.04 (0.33), residues: 250 loop : -0.71 (0.30), residues: 439 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 0.020 0.001 TYR R 130 ARG 0.003 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 113 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7692 (mt) cc_final: 0.7421 (mt) REVERT: A 299 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6526 (mm-30) REVERT: A 392 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: B 170 ASP cc_start: 0.8029 (t70) cc_final: 0.7496 (t70) REVERT: B 175 GLN cc_start: 0.7475 (mm110) cc_final: 0.7078 (mp10) REVERT: N 34 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8430 (mmm) REVERT: N 35 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.7717 (p0) REVERT: N 53 GLN cc_start: 0.7845 (mp10) cc_final: 0.7604 (mp10) REVERT: R 34 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6361 (tm-30) REVERT: R 185 SER cc_start: 0.8003 (OUTLIER) cc_final: 0.7495 (p) REVERT: R 267 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7367 (pt0) REVERT: R 354 LYS cc_start: 0.6874 (mttt) cc_final: 0.6070 (ptmm) outliers start: 15 outliers final: 10 residues processed: 108 average time/residue: 1.3647 time to fit residues: 157.4169 Evaluate side-chains 113 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 380 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 3.9990 chunk 91 optimal weight: 0.0020 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 93 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.189026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131302 restraints weight = 9022.743| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.95 r_work: 0.3122 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9239 Z= 0.159 Angle : 0.491 7.619 12516 Z= 0.261 Chirality : 0.040 0.143 1404 Planarity : 0.003 0.053 1594 Dihedral : 3.898 19.334 1247 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.62 % Allowed : 17.36 % Favored : 81.02 % 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: 1.15 (0.26), residues: 1130 helix: 2.64 (0.25), residues: 441 sheet: -0.02 (0.33), residues: 249 loop : -0.72 (0.30), residues: 440 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 0.014 0.001 PHE A 212 TYR 0.021 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: 8146.48 seconds wall clock time: 142 minutes 6.35 seconds (8526.35 seconds total)