Starting phenix.real_space_refine on Sun Jul 27 09:16:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vbh_31879/07_2025/7vbh_31879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vbh_31879/07_2025/7vbh_31879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vbh_31879/07_2025/7vbh_31879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vbh_31879/07_2025/7vbh_31879.map" model { file = "/net/cci-nas-00/data/ceres_data/7vbh_31879/07_2025/7vbh_31879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vbh_31879/07_2025/7vbh_31879.cif" } resolution = 3.0 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= -0.003 sd= 0.089 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 53 5.16 5 C 5817 2.51 5 N 1577 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9116 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1761 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 3 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3105 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 6.04, per 1000 atoms: 0.66 Number of scatterers: 9116 At special positions: 0 Unit cell: (81.396, 96.39, 170.289, 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 53 16.00 O 1669 8.00 N 1577 7.00 C 5817 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=2.04 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.04 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 41.2% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.661A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.834A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.660A pdb=" N LEU A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.756A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.750A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 removed outlier: 3.628A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.566A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 28 removed outlier: 3.993A pdb=" N ASP P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 51 removed outlier: 3.715A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 168 Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.727A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 214 Processing helix chain 'R' and resid 219 through 222 Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.813A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 291 removed outlier: 3.538A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 336 removed outlier: 3.541A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 365 Processing helix chain 'R' and resid 377 through 403 removed outlier: 3.862A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE R 382 " --> pdb=" O THR R 378 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE R 390 " --> pdb=" O THR R 386 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA R 399 " --> pdb=" O GLY R 395 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 422 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.642A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 22 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.589A pdb=" N GLU G 58 " --> pdb=" O PRO G 55 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 55 through 59' Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.322A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.563A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.543A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.382A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.736A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.075A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.643A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.687A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.135A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.845A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1263 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: 2.49 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1478 1.29 - 1.42: 2571 1.42 - 1.56: 5198 1.56 - 1.69: 3 1.69 - 1.83: 72 Bond restraints: 9322 Sorted by residual: bond pdb=" C02 D6M P 501 " pdb=" C12 D6M P 501 " ideal model delta sigma weight residual 1.517 1.795 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" C ASP B 228 " pdb=" O ASP B 228 " ideal model delta sigma weight residual 1.234 1.169 0.064 1.23e-02 6.61e+03 2.75e+01 bond pdb=" C07 D6M P 501 " pdb=" O08 D6M P 501 " ideal model delta sigma weight residual 1.247 1.154 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C SER B 227 " pdb=" O SER B 227 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.28e-02 6.10e+03 1.97e+01 bond pdb=" N SER B 227 " pdb=" CA SER B 227 " ideal model delta sigma weight residual 1.455 1.394 0.061 1.41e-02 5.03e+03 1.87e+01 ... (remaining 9317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 12176 2.49 - 4.99: 379 4.99 - 7.48: 47 7.48 - 9.97: 18 9.97 - 12.47: 13 Bond angle restraints: 12633 Sorted by residual: angle pdb=" N TYR P 13 " pdb=" CA TYR P 13 " pdb=" C TYR P 13 " ideal model delta sigma weight residual 112.23 100.11 12.12 1.26e+00 6.30e-01 9.25e+01 angle pdb=" C THR P 5 " pdb=" CA THR P 5 " pdb=" CB THR P 5 " ideal model delta sigma weight residual 110.92 100.58 10.34 1.59e+00 3.96e-01 4.23e+01 angle pdb=" N PRO N 100 " pdb=" CA PRO N 100 " pdb=" C PRO N 100 " ideal model delta sigma weight residual 113.47 121.65 -8.18 1.43e+00 4.89e-01 3.28e+01 angle pdb=" N ASP B 228 " pdb=" CA ASP B 228 " pdb=" C ASP B 228 " ideal model delta sigma weight residual 110.42 118.66 -8.24 1.46e+00 4.69e-01 3.18e+01 angle pdb=" CA LYS A 305 " pdb=" CB LYS A 305 " pdb=" CG LYS A 305 " ideal model delta sigma weight residual 114.10 125.33 -11.23 2.00e+00 2.50e-01 3.15e+01 ... (remaining 12628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4867 17.97 - 35.95: 521 35.95 - 53.92: 90 53.92 - 71.90: 27 71.90 - 89.87: 12 Dihedral angle restraints: 5517 sinusoidal: 2193 harmonic: 3324 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual -86.00 -160.71 74.71 1 1.00e+01 1.00e-02 7.07e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 44.87 48.13 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CA GLU A 327 " pdb=" C GLU A 327 " pdb=" N PRO A 328 " pdb=" CA PRO A 328 " ideal model delta harmonic sigma weight residual 180.00 -151.95 -28.05 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 5514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1154 0.077 - 0.155: 209 0.155 - 0.232: 24 0.232 - 0.310: 2 0.310 - 0.387: 3 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CA ASP B 228 " pdb=" N ASP B 228 " pdb=" C ASP B 228 " pdb=" CB ASP B 228 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB ILE N 51 " pdb=" CA ILE N 51 " pdb=" CG1 ILE N 51 " pdb=" CG2 ILE N 51 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA PRO N 100 " pdb=" N PRO N 100 " pdb=" C PRO N 100 " pdb=" CB PRO N 100 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1389 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 D6M P 501 " -0.095 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C04 D6M P 501 " 0.348 2.00e-02 2.50e+03 pdb=" C12 D6M P 501 " 0.123 2.00e-02 2.50e+03 pdb=" N03 D6M P 501 " -0.518 2.00e-02 2.50e+03 pdb=" O01 D6M P 501 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 385 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C PHE R 385 " 0.064 2.00e-02 2.50e+03 pdb=" O PHE R 385 " -0.024 2.00e-02 2.50e+03 pdb=" N THR R 386 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 226 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C GLU B 226 " 0.059 2.00e-02 2.50e+03 pdb=" O GLU B 226 " -0.021 2.00e-02 2.50e+03 pdb=" N SER B 227 " -0.021 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 41 2.41 - 3.03: 4872 3.03 - 3.65: 14461 3.65 - 4.28: 22223 4.28 - 4.90: 37221 Nonbonded interactions: 78818 Sorted by model distance: nonbonded pdb=" O LEU P 27 " pdb=" NH2 ARG R 121 " model vdw 1.784 3.120 nonbonded pdb=" CD2 LEU P 26 " pdb=" O GLU R 68 " model vdw 1.908 3.460 nonbonded pdb=" OD1 ASP P 15 " pdb=" N LEU R 32 " model vdw 1.947 3.120 nonbonded pdb=" N HIS P 1 " pdb=" CH2 TRP R 306 " model vdw 1.950 3.420 nonbonded pdb=" O GLY P 29 " pdb=" OE2 GLU R 68 " model vdw 2.182 3.040 ... (remaining 78813 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.290 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 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 : 0.010 0.278 9329 Z= 0.483 Angle : 1.119 12.466 12645 Z= 0.621 Chirality : 0.062 0.387 1392 Planarity : 0.011 0.294 1604 Dihedral : 15.915 89.873 3349 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.52 % Allowed : 9.91 % Favored : 89.58 % Cbeta Deviations : 0.09 % 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: -4.06 (0.19), residues: 1117 helix: -2.58 (0.18), residues: 439 sheet: -2.61 (0.29), residues: 212 loop : -2.66 (0.23), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP R 214 HIS 0.010 0.002 HIS A 357 PHE 0.034 0.003 PHE B 151 TYR 0.025 0.003 TYR R 148 ARG 0.009 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.18185 ( 441) hydrogen bonds : angle 8.36656 ( 1263) SS BOND : bond 0.00403 ( 6) SS BOND : angle 2.20183 ( 12) covalent geometry : bond 0.01029 ( 9322) covalent geometry : angle 1.11731 (12633) Misc. bond : bond 0.10469 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 166 average time/residue: 1.3505 time to fit residues: 242.3063 Evaluate side-chains 91 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 239 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 87 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN P 20 GLN ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 ASN R 304 ASN R 320 ASN R 394 GLN B 9 GLN B 35 ASN B 155 ASN B 176 GLN B 237 ASN B 259 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.218296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.177257 restraints weight = 10688.230| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.44 r_work: 0.3742 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9329 Z= 0.167 Angle : 0.684 8.636 12645 Z= 0.356 Chirality : 0.043 0.152 1392 Planarity : 0.006 0.064 1604 Dihedral : 7.138 58.528 1279 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.76 % Favored : 96.15 % Rotamer: Outliers : 3.41 % Allowed : 16.82 % Favored : 79.77 % 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: -1.88 (0.23), residues: 1117 helix: 0.03 (0.24), residues: 435 sheet: -1.81 (0.31), residues: 205 loop : -2.15 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 72 HIS 0.005 0.001 HIS A 362 PHE 0.014 0.002 PHE B 151 TYR 0.027 0.002 TYR R 148 ARG 0.007 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 441) hydrogen bonds : angle 5.17877 ( 1263) SS BOND : bond 0.00519 ( 6) SS BOND : angle 1.31557 ( 12) covalent geometry : bond 0.00371 ( 9322) covalent geometry : angle 0.68287 (12633) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8240 (m-30) cc_final: 0.8023 (m-30) REVERT: A 392 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7331 (mt-10) REVERT: N 52 SER cc_start: 0.8591 (p) cc_final: 0.7982 (t) REVERT: N 53 GLN cc_start: 0.7611 (mp10) cc_final: 0.7360 (mp10) REVERT: R 34 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7501 (tm-30) REVERT: R 287 VAL cc_start: 0.5864 (t) cc_final: 0.5646 (p) REVERT: R 293 ASP cc_start: 0.5455 (p0) cc_final: 0.4681 (t0) REVERT: R 320 ASN cc_start: 0.6976 (OUTLIER) cc_final: 0.6266 (m-40) REVERT: B 259 GLN cc_start: 0.6014 (pt0) cc_final: 0.5736 (pt0) REVERT: G 38 MET cc_start: 0.6211 (tmm) cc_final: 0.5716 (ttp) outliers start: 33 outliers final: 10 residues processed: 155 average time/residue: 1.0202 time to fit residues: 171.1058 Evaluate side-chains 115 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 320 ASN Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN N 39 GLN P 1 HIS ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 GLN B 88 ASN B 220 GLN B 230 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.197087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.153131 restraints weight = 10581.732| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.96 r_work: 0.3457 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9329 Z= 0.191 Angle : 0.686 12.688 12645 Z= 0.359 Chirality : 0.046 0.200 1392 Planarity : 0.006 0.090 1604 Dihedral : 6.180 58.475 1273 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.02 % Allowed : 18.68 % Favored : 77.30 % 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: -1.23 (0.24), residues: 1117 helix: 0.76 (0.25), residues: 441 sheet: -1.42 (0.32), residues: 213 loop : -2.08 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 243 HIS 0.007 0.001 HIS A 220 PHE 0.027 0.002 PHE B 151 TYR 0.023 0.002 TYR R 148 ARG 0.007 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.05183 ( 441) hydrogen bonds : angle 4.83374 ( 1263) SS BOND : bond 0.00429 ( 6) SS BOND : angle 1.86682 ( 12) covalent geometry : bond 0.00438 ( 9322) covalent geometry : angle 0.68440 (12633) Misc. bond : bond 0.00334 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 THR cc_start: 0.7108 (OUTLIER) cc_final: 0.6741 (m) REVERT: A 380 ARG cc_start: 0.7525 (ttp-110) cc_final: 0.6685 (mtp85) REVERT: A 392 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7297 (mt-10) REVERT: N 94 TYR cc_start: 0.8014 (m-80) cc_final: 0.7780 (m-80) REVERT: P 21 ASP cc_start: 0.8157 (t70) cc_final: 0.7837 (t70) REVERT: R 139 GLU cc_start: 0.7115 (pm20) cc_final: 0.6338 (tp30) REVERT: R 202 LYS cc_start: 0.6247 (ttpp) cc_final: 0.5938 (tptp) REVERT: R 292 GLU cc_start: 0.7488 (tp30) cc_final: 0.6805 (mp0) REVERT: R 346 LYS cc_start: 0.7949 (mtmm) cc_final: 0.7694 (mtpm) REVERT: B 17 GLN cc_start: 0.6700 (tm-30) cc_final: 0.6425 (tm-30) REVERT: B 46 ARG cc_start: 0.8275 (mtp-110) cc_final: 0.8020 (mtm180) REVERT: B 215 GLU cc_start: 0.8025 (mp0) cc_final: 0.7779 (tt0) REVERT: B 260 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6517 (tt0) REVERT: G 44 HIS cc_start: 0.6405 (m90) cc_final: 0.6172 (m90) outliers start: 39 outliers final: 14 residues processed: 163 average time/residue: 1.0990 time to fit residues: 192.7297 Evaluate side-chains 125 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 267 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 73 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 213 GLN B 230 ASN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.195442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.152348 restraints weight = 10413.341| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.80 r_work: 0.3349 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9329 Z= 0.151 Angle : 0.602 8.130 12645 Z= 0.317 Chirality : 0.043 0.160 1392 Planarity : 0.004 0.058 1604 Dihedral : 5.785 57.317 1273 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.02 % Allowed : 20.85 % Favored : 75.13 % 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: -0.56 (0.25), residues: 1117 helix: 1.40 (0.25), residues: 438 sheet: -0.89 (0.34), residues: 218 loop : -1.88 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 243 HIS 0.007 0.001 HIS R 171 PHE 0.018 0.001 PHE B 151 TYR 0.020 0.002 TYR R 148 ARG 0.004 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 441) hydrogen bonds : angle 4.51428 ( 1263) SS BOND : bond 0.00336 ( 6) SS BOND : angle 1.23326 ( 12) covalent geometry : bond 0.00343 ( 9322) covalent geometry : angle 0.60076 (12633) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8379 (tttt) cc_final: 0.7973 (mmpt) REVERT: A 266 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7852 (tm) REVERT: A 380 ARG cc_start: 0.7480 (ttp-110) cc_final: 0.6574 (mtp85) REVERT: A 392 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7257 (mt-10) REVERT: R 139 GLU cc_start: 0.7275 (pm20) cc_final: 0.6595 (tp30) REVERT: R 192 LEU cc_start: 0.8302 (tt) cc_final: 0.7755 (mp) REVERT: R 202 LYS cc_start: 0.6402 (ttpp) cc_final: 0.5962 (tptp) REVERT: R 292 GLU cc_start: 0.7925 (tp30) cc_final: 0.7689 (mp0) REVERT: R 346 LYS cc_start: 0.7966 (mtmm) cc_final: 0.7739 (mtpm) REVERT: B 17 GLN cc_start: 0.6902 (tm-30) cc_final: 0.6601 (tm-30) REVERT: B 46 ARG cc_start: 0.8267 (mtp-110) cc_final: 0.7856 (mtp-110) outliers start: 39 outliers final: 14 residues processed: 156 average time/residue: 1.0975 time to fit residues: 184.6093 Evaluate side-chains 128 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 105 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN R 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.190720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.148979 restraints weight = 10465.295| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.56 r_work: 0.3308 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9329 Z= 0.196 Angle : 0.658 9.003 12645 Z= 0.342 Chirality : 0.045 0.164 1392 Planarity : 0.004 0.056 1604 Dihedral : 5.846 56.640 1273 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.64 % Allowed : 21.26 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.54 (0.25), residues: 1117 helix: 1.40 (0.25), residues: 443 sheet: -0.74 (0.34), residues: 222 loop : -1.98 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 243 HIS 0.009 0.001 HIS R 171 PHE 0.018 0.002 PHE N 108 TYR 0.024 0.002 TYR R 289 ARG 0.004 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.05076 ( 441) hydrogen bonds : angle 4.58574 ( 1263) SS BOND : bond 0.00758 ( 6) SS BOND : angle 2.15050 ( 12) covalent geometry : bond 0.00455 ( 9322) covalent geometry : angle 0.65450 (12633) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8519 (tttt) cc_final: 0.8119 (mmpt) REVERT: A 266 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8101 (tm) REVERT: A 372 ILE cc_start: 0.8511 (mm) cc_final: 0.8303 (mp) REVERT: A 380 ARG cc_start: 0.7636 (ttp-110) cc_final: 0.6738 (mtp85) REVERT: A 386 MET cc_start: 0.7973 (ppp) cc_final: 0.7759 (ptm) REVERT: A 392 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7271 (mt-10) REVERT: R 154 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8413 (mp) REVERT: R 192 LEU cc_start: 0.8421 (tt) cc_final: 0.7903 (mp) REVERT: R 202 LYS cc_start: 0.7199 (ttpp) cc_final: 0.6726 (tptp) REVERT: R 271 SER cc_start: 0.8411 (t) cc_final: 0.7971 (m) REVERT: R 346 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7933 (mtpm) REVERT: B 118 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6804 (p0) REVERT: B 186 ASP cc_start: 0.7653 (m-30) cc_final: 0.7354 (m-30) outliers start: 45 outliers final: 22 residues processed: 168 average time/residue: 1.5945 time to fit residues: 289.6299 Evaluate side-chains 151 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 98 optimal weight: 0.0670 chunk 42 optimal weight: 20.0000 chunk 28 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 77 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN R 171 HIS B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.201505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.158608 restraints weight = 10215.827| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.34 r_work: 0.3589 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.7064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9329 Z= 0.120 Angle : 0.579 8.148 12645 Z= 0.301 Chirality : 0.042 0.149 1392 Planarity : 0.004 0.056 1604 Dihedral : 5.532 55.905 1273 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.10 % Allowed : 23.74 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1117 helix: 1.78 (0.25), residues: 438 sheet: -0.58 (0.35), residues: 224 loop : -1.78 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.006 0.001 HIS R 171 PHE 0.015 0.001 PHE R 280 TYR 0.024 0.002 TYR R 289 ARG 0.004 0.000 ARG R 43 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 441) hydrogen bonds : angle 4.23944 ( 1263) SS BOND : bond 0.00619 ( 6) SS BOND : angle 1.79396 ( 12) covalent geometry : bond 0.00270 ( 9322) covalent geometry : angle 0.57627 (12633) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8497 (tttt) cc_final: 0.8187 (mmpt) REVERT: A 266 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8056 (tm) REVERT: A 380 ARG cc_start: 0.7508 (ttp-110) cc_final: 0.6749 (mtp85) REVERT: A 386 MET cc_start: 0.7819 (ppp) cc_final: 0.7583 (ptm) REVERT: A 392 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7323 (mm-30) REVERT: N 3 GLN cc_start: 0.6979 (tp-100) cc_final: 0.6710 (tp40) REVERT: R 192 LEU cc_start: 0.8370 (tt) cc_final: 0.7951 (mp) REVERT: R 202 LYS cc_start: 0.7085 (ttpp) cc_final: 0.6694 (tptp) REVERT: R 271 SER cc_start: 0.8465 (t) cc_final: 0.8009 (m) REVERT: R 289 TYR cc_start: 0.7384 (t80) cc_final: 0.7105 (t80) REVERT: R 346 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7989 (mtpm) outliers start: 30 outliers final: 15 residues processed: 156 average time/residue: 1.0211 time to fit residues: 172.1861 Evaluate side-chains 142 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 0.0670 chunk 71 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN R 171 HIS R 263 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.198100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154430 restraints weight = 10386.457| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.62 r_work: 0.3554 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.7306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9329 Z= 0.165 Angle : 0.616 8.466 12645 Z= 0.322 Chirality : 0.043 0.158 1392 Planarity : 0.004 0.054 1604 Dihedral : 5.615 56.362 1273 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.41 % Allowed : 24.36 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.16 (0.26), residues: 1117 helix: 1.80 (0.25), residues: 434 sheet: -0.58 (0.35), residues: 223 loop : -1.77 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 243 HIS 0.006 0.001 HIS A 220 PHE 0.014 0.002 PHE N 108 TYR 0.019 0.002 TYR R 148 ARG 0.004 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 441) hydrogen bonds : angle 4.36408 ( 1263) SS BOND : bond 0.00550 ( 6) SS BOND : angle 1.80759 ( 12) covalent geometry : bond 0.00388 ( 9322) covalent geometry : angle 0.61412 (12633) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8609 (tttt) cc_final: 0.8182 (mmpt) REVERT: A 266 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8226 (tm) REVERT: A 372 ILE cc_start: 0.8590 (mm) cc_final: 0.8383 (mp) REVERT: A 380 ARG cc_start: 0.7837 (ttp-110) cc_final: 0.6905 (mtp85) REVERT: A 386 MET cc_start: 0.8171 (ppp) cc_final: 0.7942 (ptm) REVERT: A 392 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7434 (mm-30) REVERT: N 87 LYS cc_start: 0.7520 (mttm) cc_final: 0.6937 (mtpm) REVERT: R 202 LYS cc_start: 0.7357 (ttpp) cc_final: 0.6936 (tptp) REVERT: R 271 SER cc_start: 0.8609 (t) cc_final: 0.8164 (m) REVERT: R 289 TYR cc_start: 0.7556 (t80) cc_final: 0.7238 (t80) REVERT: R 346 LYS cc_start: 0.8179 (mtmm) cc_final: 0.7916 (mtpm) REVERT: B 57 LYS cc_start: 0.9255 (pttm) cc_final: 0.9053 (pttp) REVERT: B 96 ARG cc_start: 0.7532 (mtm110) cc_final: 0.7274 (mtm-85) REVERT: B 118 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6960 (p0) REVERT: G 21 MET cc_start: 0.4604 (ttt) cc_final: 0.4325 (mmm) outliers start: 33 outliers final: 22 residues processed: 149 average time/residue: 1.0193 time to fit residues: 165.1461 Evaluate side-chains 149 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.197336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154229 restraints weight = 10464.180| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.86 r_work: 0.3539 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.7600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9329 Z= 0.170 Angle : 0.632 8.548 12645 Z= 0.328 Chirality : 0.044 0.160 1392 Planarity : 0.004 0.054 1604 Dihedral : 5.683 57.386 1273 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.72 % Allowed : 23.32 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.17 (0.25), residues: 1117 helix: 1.66 (0.25), residues: 449 sheet: -0.39 (0.35), residues: 221 loop : -1.88 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 214 HIS 0.006 0.001 HIS A 220 PHE 0.014 0.002 PHE N 108 TYR 0.034 0.002 TYR R 220 ARG 0.009 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 441) hydrogen bonds : angle 4.38688 ( 1263) SS BOND : bond 0.00452 ( 6) SS BOND : angle 1.72078 ( 12) covalent geometry : bond 0.00396 ( 9322) covalent geometry : angle 0.63027 (12633) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8628 (tttt) cc_final: 0.8213 (mmpt) REVERT: A 266 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8258 (tm) REVERT: A 372 ILE cc_start: 0.8608 (mm) cc_final: 0.8397 (mp) REVERT: A 380 ARG cc_start: 0.7847 (ttp-110) cc_final: 0.6905 (mtp85) REVERT: A 386 MET cc_start: 0.8175 (ppp) cc_final: 0.7933 (ptm) REVERT: A 392 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7431 (mm-30) REVERT: N 87 LYS cc_start: 0.7596 (mttm) cc_final: 0.7092 (mtpm) REVERT: R 202 LYS cc_start: 0.7446 (ttpp) cc_final: 0.6981 (tptp) REVERT: R 271 SER cc_start: 0.8722 (t) cc_final: 0.8291 (m) REVERT: R 279 LEU cc_start: 0.8509 (tm) cc_final: 0.7769 (mp) REVERT: R 289 TYR cc_start: 0.7603 (t80) cc_final: 0.7324 (t80) REVERT: R 346 LYS cc_start: 0.8213 (mtmm) cc_final: 0.7943 (mtpm) REVERT: B 96 ARG cc_start: 0.7637 (mtm110) cc_final: 0.7352 (mtm-85) REVERT: B 118 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6940 (p0) outliers start: 36 outliers final: 22 residues processed: 151 average time/residue: 0.9555 time to fit residues: 156.7825 Evaluate side-chains 148 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 0.0000 chunk 34 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.198674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.155509 restraints weight = 10301.747| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.87 r_work: 0.3552 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.7771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9329 Z= 0.132 Angle : 0.592 8.741 12645 Z= 0.309 Chirality : 0.042 0.160 1392 Planarity : 0.004 0.053 1604 Dihedral : 5.508 54.455 1273 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.99 % Allowed : 24.97 % Favored : 72.03 % 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: 0.06 (0.26), residues: 1117 helix: 1.98 (0.25), residues: 438 sheet: -0.34 (0.35), residues: 221 loop : -1.76 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 39 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.001 PHE R 280 TYR 0.024 0.002 TYR R 220 ARG 0.006 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 441) hydrogen bonds : angle 4.24796 ( 1263) SS BOND : bond 0.00442 ( 6) SS BOND : angle 1.53669 ( 12) covalent geometry : bond 0.00299 ( 9322) covalent geometry : angle 0.59002 (12633) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8514 (tttt) cc_final: 0.8194 (mmpt) REVERT: A 266 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8144 (tm) REVERT: A 380 ARG cc_start: 0.7584 (ttp-110) cc_final: 0.6731 (mtp85) REVERT: A 386 MET cc_start: 0.7813 (ppp) cc_final: 0.7544 (ptm) REVERT: A 392 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7210 (mm-30) REVERT: N 87 LYS cc_start: 0.7684 (mttm) cc_final: 0.7285 (mtpm) REVERT: R 41 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8074 (tp30) REVERT: R 202 LYS cc_start: 0.7285 (ttpp) cc_final: 0.6853 (tptp) REVERT: R 271 SER cc_start: 0.8533 (t) cc_final: 0.8122 (m) REVERT: R 279 LEU cc_start: 0.8359 (tm) cc_final: 0.7670 (mp) REVERT: R 289 TYR cc_start: 0.7481 (t80) cc_final: 0.7172 (t80) REVERT: R 293 ASP cc_start: 0.7821 (t0) cc_final: 0.7563 (t0) REVERT: R 346 LYS cc_start: 0.8291 (mtmm) cc_final: 0.8029 (mtpm) REVERT: B 118 ASP cc_start: 0.6978 (OUTLIER) cc_final: 0.6589 (p0) outliers start: 29 outliers final: 21 residues processed: 151 average time/residue: 1.0853 time to fit residues: 177.3812 Evaluate side-chains 148 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 108 optimal weight: 0.4980 chunk 41 optimal weight: 0.0000 chunk 29 optimal weight: 2.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.198528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.158261 restraints weight = 10326.170| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.32 r_work: 0.3594 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.7879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9329 Z= 0.128 Angle : 0.610 9.544 12645 Z= 0.317 Chirality : 0.042 0.156 1392 Planarity : 0.004 0.053 1604 Dihedral : 5.434 54.980 1273 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.58 % Allowed : 25.39 % Favored : 72.03 % 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: 0.20 (0.26), residues: 1117 helix: 2.12 (0.25), residues: 438 sheet: -0.22 (0.35), residues: 222 loop : -1.74 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.001 PHE R 280 TYR 0.018 0.002 TYR R 148 ARG 0.002 0.000 ARG R 376 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 441) hydrogen bonds : angle 4.17595 ( 1263) SS BOND : bond 0.00413 ( 6) SS BOND : angle 1.48044 ( 12) covalent geometry : bond 0.00290 ( 9322) covalent geometry : angle 0.60870 (12633) Misc. bond : bond 0.00004 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.957 Fit side-chains REVERT: A 32 LYS cc_start: 0.8571 (tttt) cc_final: 0.8161 (mmpt) REVERT: A 266 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8250 (tm) REVERT: A 380 ARG cc_start: 0.7802 (ttp-110) cc_final: 0.6919 (mtp85) REVERT: A 386 MET cc_start: 0.8102 (ppp) cc_final: 0.7892 (ptm) REVERT: A 392 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7348 (mm-30) REVERT: N 87 LYS cc_start: 0.7693 (mttm) cc_final: 0.7289 (mtpm) REVERT: R 41 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8212 (tp30) REVERT: R 202 LYS cc_start: 0.7373 (ttpp) cc_final: 0.6954 (tptp) REVERT: R 271 SER cc_start: 0.8690 (t) cc_final: 0.8241 (m) REVERT: R 279 LEU cc_start: 0.8313 (tm) cc_final: 0.7599 (mp) REVERT: R 289 TYR cc_start: 0.7578 (t80) cc_final: 0.7270 (t80) REVERT: R 293 ASP cc_start: 0.8010 (t0) cc_final: 0.7762 (t0) REVERT: R 346 LYS cc_start: 0.8241 (mtmm) cc_final: 0.7981 (mtpm) outliers start: 25 outliers final: 22 residues processed: 145 average time/residue: 1.2484 time to fit residues: 196.2396 Evaluate side-chains 147 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 1 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS R 213 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.197972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155198 restraints weight = 10340.455| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.89 r_work: 0.3540 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.7996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9329 Z= 0.149 Angle : 0.626 8.834 12645 Z= 0.323 Chirality : 0.043 0.268 1392 Planarity : 0.004 0.053 1604 Dihedral : 5.507 57.932 1273 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.89 % Allowed : 25.28 % Favored : 71.83 % 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: 0.23 (0.26), residues: 1117 helix: 2.13 (0.25), residues: 437 sheet: -0.27 (0.35), residues: 228 loop : -1.68 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 214 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.001 PHE R 280 TYR 0.026 0.002 TYR B 264 ARG 0.006 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 441) hydrogen bonds : angle 4.24188 ( 1263) SS BOND : bond 0.00389 ( 6) SS BOND : angle 1.55156 ( 12) covalent geometry : bond 0.00346 ( 9322) covalent geometry : angle 0.62438 (12633) Misc. bond : bond 0.00006 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7699.88 seconds wall clock time: 137 minutes 16.72 seconds (8236.72 seconds total)