Starting phenix.real_space_refine on Thu Feb 13 07:49:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rtb_24680/02_2025/7rtb_24680.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtb_24680/02_2025/7rtb_24680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rtb_24680/02_2025/7rtb_24680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtb_24680/02_2025/7rtb_24680.map" model { file = "/net/cci-nas-00/data/ceres_data/7rtb_24680/02_2025/7rtb_24680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtb_24680/02_2025/7rtb_24680.cif" } resolution = 2.14 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= 0.023 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: 5 Type Number sf(0) Gaussians S 51 5.16 5 C 5693 2.51 5 N 1568 2.21 5 O 1660 1.98 5 H 7 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8979 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1949 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} 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: "R" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2796 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 14, 'TRANS': 369} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 419 Unresolved non-hydrogen angles: 553 Unresolved non-hydrogen dihedrals: 377 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 8, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 277 Chain: "P" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 243 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.00, per 1000 atoms: 0.67 Number of scatterers: 8979 At special positions: 0 Unit cell: (81.9, 96.85, 170.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 O 1660 8.00 N 1568 7.00 C 5693 6.00 H 7 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 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=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 12 sheets defined 44.2% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 3.883A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.516A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.563A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 removed outlier: 4.415A pdb=" N TYR A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.610A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.688A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.657A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.970A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.605A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.854A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.748A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 53 removed outlier: 3.640A pdb=" N GLN R 37 " --> pdb=" O TRP R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 93 removed outlier: 4.172A pdb=" N SER R 93 " --> pdb=" O PRO R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 169 removed outlier: 3.612A pdb=" N ILE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 199 Processing helix chain 'R' and resid 199 through 211 removed outlier: 3.859A pdb=" N THR R 207 " --> pdb=" O TRP R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 223 Processing helix chain 'R' and resid 225 through 257 removed outlier: 3.581A pdb=" N VAL R 229 " --> pdb=" O SER R 225 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU R 231 " --> pdb=" O ARG R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 291 removed outlier: 3.695A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix removed outlier: 3.782A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.650A pdb=" N TYR R 289 " --> pdb=" O GLY R 285 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR R 291 " --> pdb=" O VAL R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 298 removed outlier: 4.088A pdb=" N CYS R 296 " --> pdb=" O ASP R 293 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP R 297 " --> pdb=" O GLU R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 308 removed outlier: 3.603A pdb=" N LEU R 307 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE R 308 " --> pdb=" O TYR R 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 304 through 308' Processing helix chain 'R' and resid 309 through 338 removed outlier: 3.823A pdb=" N ASN R 320 " --> pdb=" O ALA R 316 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU R 322 " --> pdb=" O GLY R 318 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE R 324 " --> pdb=" O ASN R 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 341 through 361 removed outlier: 3.703A pdb=" N LEU R 354 " --> pdb=" O ALA R 350 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 371 Processing helix chain 'R' and resid 382 through 403 removed outlier: 5.104A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 423 removed outlier: 4.056A pdb=" N TRP R 420 " --> pdb=" O SER R 416 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 26 Processing helix chain 'P' and resid 27 through 29 No H-bonds generated for 'chain 'P' and resid 27 through 29' Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.396A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.769A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.968A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.083A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.511A 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: 3.582A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.673A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.571A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.672A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.593A 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 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.679A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 65 through 66 removed outlier: 3.527A pdb=" N THR R 65 " --> pdb=" O TRP R 72 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP R 72 " --> pdb=" O THR R 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'R' and resid 80 through 84 472 hydrogen bonds defined for protein. 1350 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: 2.87 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 7 1.09 - 1.27: 1478 1.27 - 1.45: 2572 1.45 - 1.63: 5026 1.63 - 1.81: 71 Bond restraints: 9154 Sorted by residual: bond pdb=" C ALA B 106 " pdb=" N PRO B 107 " ideal model delta sigma weight residual 1.333 1.379 -0.046 1.44e-02 4.82e+03 1.01e+01 bond pdb=" N ILE P 12 " pdb=" CA ILE P 12 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.82e+00 bond pdb=" N VAL P 23 " pdb=" CA VAL P 23 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.30e-02 5.92e+03 6.66e+00 bond pdb=" N ASN R 320 " pdb=" CA ASN R 320 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.36e+00 bond pdb=" N LEU P 26 " pdb=" CA LEU P 26 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.30e+00 ... (remaining 9149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 11767 1.15 - 2.30: 497 2.30 - 3.46: 130 3.46 - 4.61: 19 4.61 - 5.76: 7 Bond angle restraints: 12420 Sorted by residual: angle pdb=" C ALA B 106 " pdb=" N PRO B 107 " pdb=" CA PRO B 107 " ideal model delta sigma weight residual 119.47 125.13 -5.66 1.16e+00 7.43e-01 2.38e+01 angle pdb=" C GLY R 275 " pdb=" N VAL R 276 " pdb=" CA VAL R 276 " ideal model delta sigma weight residual 120.24 122.75 -2.51 6.30e-01 2.52e+00 1.59e+01 angle pdb=" N ASN P 24 " pdb=" CA ASN P 24 " pdb=" C ASN P 24 " ideal model delta sigma weight residual 111.28 107.62 3.66 1.09e+00 8.42e-01 1.13e+01 angle pdb=" N TRP R 417 " pdb=" CA TRP R 417 " pdb=" C TRP R 417 " ideal model delta sigma weight residual 113.55 109.58 3.97 1.26e+00 6.30e-01 9.92e+00 angle pdb=" C VAL R 276 " pdb=" CA VAL R 276 " pdb=" CB VAL R 276 " ideal model delta sigma weight residual 114.35 111.21 3.14 1.06e+00 8.90e-01 8.80e+00 ... (remaining 12415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4922 17.92 - 35.85: 389 35.85 - 53.77: 79 53.77 - 71.70: 17 71.70 - 89.62: 13 Dihedral angle restraints: 5420 sinusoidal: 2019 harmonic: 3401 Sorted by residual: dihedral pdb=" CA ASN R 320 " pdb=" C ASN R 320 " pdb=" N PHE R 321 " pdb=" CA PHE R 321 " ideal model delta harmonic sigma weight residual 180.00 157.67 22.33 0 5.00e+00 4.00e-02 1.99e+01 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 -86.00 -120.51 34.51 1 1.00e+01 1.00e-02 1.69e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 163.17 16.83 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1084 0.045 - 0.090: 231 0.090 - 0.135: 73 0.135 - 0.180: 11 0.180 - 0.226: 2 Chirality restraints: 1401 Sorted by residual: chirality pdb=" CA LYS P 16 " pdb=" N LYS P 16 " pdb=" C LYS P 16 " pdb=" CB LYS P 16 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA LEU P 14 " pdb=" N LEU P 14 " pdb=" C LEU P 14 " pdb=" CB LEU P 14 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA LYS R 202 " pdb=" N LYS R 202 " pdb=" C LYS R 202 " pdb=" CB LYS R 202 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1398 not shown) Planarity restraints: 1589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA P 19 " -0.012 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" N AIB P 20 " 0.037 2.00e-02 2.50e+03 pdb=" CA AIB P 20 " -0.010 2.00e-02 2.50e+03 pdb=" H AIB P 20 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO N 88 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 315 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.33e+00 pdb=" C PHE R 315 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE R 315 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA R 316 " -0.009 2.00e-02 2.50e+03 ... (remaining 1586 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.64: 88 2.64 - 3.13: 6623 3.13 - 3.62: 11012 3.62 - 4.11: 15348 4.11 - 4.60: 22943 Nonbonded interactions: 56014 Sorted by model distance: nonbonded pdb=" H AIB P 20 " pdb="HB22 AIB P 20 " model vdw 2.151 2.270 nonbonded pdb=" O LEU R 172 " pdb=" ND2 ASN R 177 " model vdw 2.277 2.950 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.311 2.800 nonbonded pdb="HB12 AIB P 20 " pdb="HB23 AIB P 20 " model vdw 2.328 2.440 nonbonded pdb=" NH2 ARG A 228 " pdb=" OE1 GLU A 230 " model vdw 2.335 2.950 ... (remaining 56009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.280 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.240 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 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 : 0.003 0.046 9147 Z= 0.189 Angle : 0.568 5.760 12406 Z= 0.386 Chirality : 0.043 0.226 1401 Planarity : 0.003 0.046 1588 Dihedral : 14.485 89.621 3208 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.77 % Allowed : 8.96 % Favored : 90.27 % 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: -0.80 (0.23), residues: 1144 helix: 0.35 (0.23), residues: 459 sheet: -0.46 (0.32), residues: 232 loop : -1.40 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.000 HIS A 357 PHE 0.009 0.001 PHE A 212 TYR 0.011 0.001 TYR P 13 ARG 0.002 0.000 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 186 ASP cc_start: 0.7105 (m-30) cc_final: 0.6851 (m-30) outliers start: 7 outliers final: 3 residues processed: 164 average time/residue: 1.4037 time to fit residues: 244.3844 Evaluate side-chains 114 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 0.0040 chunk 103 optimal weight: 5.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 213 GLN A 218 ASN A 254 ASN A 292 ASN B 36 ASN B 44 GLN B 175 GLN B 259 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 31 ASN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.195287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.141133 restraints weight = 10577.104| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.89 r_work: 0.3706 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9147 Z= 0.115 Angle : 0.396 3.978 12406 Z= 0.221 Chirality : 0.037 0.126 1401 Planarity : 0.003 0.034 1588 Dihedral : 3.668 32.040 1273 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.99 % Allowed : 14.93 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1144 helix: 2.26 (0.25), residues: 457 sheet: 0.04 (0.32), residues: 243 loop : -0.53 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.012 0.001 TYR P 13 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6914 (mtm110) cc_final: 0.6621 (mtp85) REVERT: A 314 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6081 (mp0) REVERT: B 42 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6153 (mmt180) REVERT: B 186 ASP cc_start: 0.8257 (m-30) cc_final: 0.7944 (m-30) REVERT: N 34 MET cc_start: 0.7883 (mmm) cc_final: 0.7345 (mmm) REVERT: R 362 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7175 (p) outliers start: 27 outliers final: 9 residues processed: 131 average time/residue: 1.4727 time to fit residues: 204.2921 Evaluate side-chains 121 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 391 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 26 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 50.0000 chunk 38 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 109 optimal weight: 0.3980 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 213 GLN A 267 GLN B 44 GLN B 110 ASN B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 39 GLN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.188800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.132051 restraints weight = 10583.628| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.91 r_work: 0.3595 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9147 Z= 0.244 Angle : 0.513 5.624 12406 Z= 0.284 Chirality : 0.041 0.137 1401 Planarity : 0.004 0.033 1588 Dihedral : 4.325 37.277 1270 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.76 % Allowed : 15.82 % Favored : 80.42 % 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: 1.25 (0.25), residues: 1144 helix: 2.45 (0.24), residues: 458 sheet: 0.16 (0.33), residues: 224 loop : -0.46 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.008 0.002 HIS A 357 PHE 0.015 0.002 PHE A 212 TYR 0.015 0.002 TYR R 235 ARG 0.007 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 1.039 Fit side-chains REVERT: B 42 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6307 (mmt180) REVERT: B 85 TYR cc_start: 0.7325 (m-10) cc_final: 0.6936 (m-10) REVERT: B 215 GLU cc_start: 0.8096 (mp0) cc_final: 0.7891 (mt-10) REVERT: B 217 MET cc_start: 0.8573 (ppp) cc_final: 0.8307 (pp-130) outliers start: 34 outliers final: 18 residues processed: 140 average time/residue: 1.3679 time to fit residues: 203.6483 Evaluate side-chains 137 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 390 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 89 optimal weight: 0.0470 chunk 49 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 213 GLN B 44 GLN B 175 GLN B 176 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 35 ASN N 77 ASN N 120 GLN ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.188774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.132040 restraints weight = 10556.324| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.90 r_work: 0.3591 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9147 Z= 0.199 Angle : 0.470 4.832 12406 Z= 0.261 Chirality : 0.040 0.136 1401 Planarity : 0.003 0.034 1588 Dihedral : 4.297 45.745 1270 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.54 % Allowed : 16.59 % Favored : 78.87 % 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: 1.42 (0.25), residues: 1144 helix: 2.67 (0.24), residues: 464 sheet: 0.29 (0.34), residues: 217 loop : -0.53 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.016 0.002 PHE B 151 TYR 0.012 0.002 TYR R 305 ARG 0.004 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 0.971 Fit side-chains REVERT: A 314 GLU cc_start: 0.6843 (tm-30) cc_final: 0.6276 (mp0) REVERT: A 343 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.6971 (m-30) REVERT: B 42 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6319 (mmt180) REVERT: B 85 TYR cc_start: 0.7312 (m-10) cc_final: 0.6944 (m-10) REVERT: B 215 GLU cc_start: 0.8100 (mp0) cc_final: 0.7833 (mt-10) REVERT: B 217 MET cc_start: 0.8583 (ppp) cc_final: 0.8326 (pp-130) REVERT: R 338 ASN cc_start: 0.5845 (m-40) cc_final: 0.5389 (t0) outliers start: 41 outliers final: 22 residues processed: 148 average time/residue: 1.3688 time to fit residues: 214.9244 Evaluate side-chains 145 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain R residue 390 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 213 GLN A 292 ASN A 357 HIS B 44 GLN B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.185158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.128207 restraints weight = 10546.481| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.88 r_work: 0.3545 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 9147 Z= 0.445 Angle : 0.667 9.518 12406 Z= 0.366 Chirality : 0.048 0.192 1401 Planarity : 0.006 0.049 1588 Dihedral : 5.129 53.699 1270 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.87 % Allowed : 17.92 % Favored : 77.21 % 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: 0.72 (0.24), residues: 1144 helix: 1.93 (0.23), residues: 458 sheet: -0.01 (0.32), residues: 230 loop : -0.75 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 234 HIS 0.008 0.002 HIS B 311 PHE 0.021 0.003 PHE B 151 TYR 0.019 0.003 TYR R 242 ARG 0.008 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 0.964 Fit side-chains REVERT: B 42 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6540 (mmp-170) REVERT: B 85 TYR cc_start: 0.7361 (m-10) cc_final: 0.6980 (m-10) REVERT: B 155 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.7155 (t0) REVERT: B 215 GLU cc_start: 0.8159 (mp0) cc_final: 0.7814 (mt-10) REVERT: N 6 GLU cc_start: 0.6687 (mp0) cc_final: 0.6477 (mp0) REVERT: N 19 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6094 (ttm170) REVERT: R 338 ASN cc_start: 0.6109 (m-40) cc_final: 0.5702 (t0) outliers start: 44 outliers final: 24 residues processed: 149 average time/residue: 1.4217 time to fit residues: 224.6106 Evaluate side-chains 144 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain R residue 390 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 25 optimal weight: 0.0670 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 213 GLN A 357 HIS B 44 GLN B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.187767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.131034 restraints weight = 10521.483| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.89 r_work: 0.3583 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9147 Z= 0.188 Angle : 0.472 4.826 12406 Z= 0.263 Chirality : 0.040 0.137 1401 Planarity : 0.003 0.039 1588 Dihedral : 4.571 55.416 1270 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.65 % Allowed : 19.03 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1144 helix: 2.61 (0.24), residues: 458 sheet: 0.20 (0.33), residues: 218 loop : -0.76 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE B 151 TYR 0.013 0.002 TYR R 305 ARG 0.008 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.127 Fit side-chains REVERT: B 42 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6432 (mmt180) REVERT: B 59 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.7870 (t80) REVERT: B 85 TYR cc_start: 0.7334 (m-10) cc_final: 0.6962 (m-10) REVERT: B 155 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.7168 (t0) REVERT: B 215 GLU cc_start: 0.8192 (mp0) cc_final: 0.7839 (mt-10) REVERT: B 217 MET cc_start: 0.8554 (ppp) cc_final: 0.8232 (pp-130) REVERT: N 6 GLU cc_start: 0.6647 (mp0) cc_final: 0.6411 (mp0) REVERT: R 338 ASN cc_start: 0.5903 (m-40) cc_final: 0.5671 (t0) outliers start: 33 outliers final: 20 residues processed: 139 average time/residue: 1.4869 time to fit residues: 218.9339 Evaluate side-chains 139 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 28 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 62 optimal weight: 0.0170 chunk 77 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 overall best weight: 2.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 357 HIS B 44 GLN B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 39 GLN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.187328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.130436 restraints weight = 10669.213| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.90 r_work: 0.3576 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9147 Z= 0.222 Angle : 0.504 5.373 12406 Z= 0.278 Chirality : 0.041 0.138 1401 Planarity : 0.004 0.041 1588 Dihedral : 4.625 55.960 1270 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.54 % Allowed : 18.58 % Favored : 76.88 % 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: 1.26 (0.25), residues: 1144 helix: 2.68 (0.24), residues: 458 sheet: 0.22 (0.33), residues: 218 loop : -0.76 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.004 0.001 HIS B 311 PHE 0.017 0.002 PHE B 151 TYR 0.014 0.002 TYR R 242 ARG 0.009 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.870 Fit side-chains REVERT: B 42 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6506 (mmt180) REVERT: B 59 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.7850 (t80) REVERT: B 85 TYR cc_start: 0.7354 (m-10) cc_final: 0.6982 (m-10) REVERT: B 155 ASN cc_start: 0.7445 (OUTLIER) cc_final: 0.7201 (t0) REVERT: B 215 GLU cc_start: 0.8188 (mp0) cc_final: 0.7819 (mt-10) REVERT: B 217 MET cc_start: 0.8560 (ppp) cc_final: 0.8233 (pp-130) REVERT: N 6 GLU cc_start: 0.6633 (mp0) cc_final: 0.6404 (mp0) REVERT: N 19 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6070 (ttm170) REVERT: R 338 ASN cc_start: 0.6052 (m-40) cc_final: 0.5760 (t0) outliers start: 41 outliers final: 23 residues processed: 144 average time/residue: 1.3662 time to fit residues: 208.8166 Evaluate side-chains 145 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 18 optimal weight: 3.9990 chunk 77 optimal weight: 50.0000 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 30.0000 chunk 48 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 49 optimal weight: 0.0030 chunk 11 optimal weight: 0.6980 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 357 HIS B 44 GLN B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.188276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.131659 restraints weight = 10686.929| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.90 r_work: 0.3593 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9147 Z= 0.156 Angle : 0.456 4.606 12406 Z= 0.252 Chirality : 0.039 0.135 1401 Planarity : 0.003 0.040 1588 Dihedral : 4.432 56.614 1270 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.09 % Allowed : 19.47 % Favored : 76.44 % 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: 1.61 (0.25), residues: 1144 helix: 3.02 (0.24), residues: 461 sheet: 0.38 (0.34), residues: 216 loop : -0.63 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.012 0.001 TYR R 242 ARG 0.009 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 1.039 Fit side-chains REVERT: A 16 GLU cc_start: 0.6695 (tp30) cc_final: 0.6486 (tp30) REVERT: A 20 ARG cc_start: 0.6932 (mtm110) cc_final: 0.6545 (mmt180) REVERT: B 42 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6378 (mmt180) REVERT: B 59 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7906 (t80) REVERT: B 85 TYR cc_start: 0.7337 (m-10) cc_final: 0.6958 (m-10) REVERT: B 155 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.7212 (t0) REVERT: B 215 GLU cc_start: 0.8181 (mp0) cc_final: 0.7829 (mt-10) REVERT: B 217 MET cc_start: 0.8550 (ppp) cc_final: 0.8226 (pp-130) REVERT: N 6 GLU cc_start: 0.6581 (mp0) cc_final: 0.6269 (mp0) REVERT: N 19 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.5995 (ttm170) REVERT: R 338 ASN cc_start: 0.5953 (m-40) cc_final: 0.5674 (t0) REVERT: R 390 PHE cc_start: 0.7560 (t80) cc_final: 0.7306 (m-80) outliers start: 37 outliers final: 24 residues processed: 142 average time/residue: 1.3625 time to fit residues: 205.7611 Evaluate side-chains 146 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 52 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 30 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 292 ASN A 357 HIS B 44 GLN B 175 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.187809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.131246 restraints weight = 10560.774| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.88 r_work: 0.3584 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9147 Z= 0.192 Angle : 0.478 5.915 12406 Z= 0.264 Chirality : 0.040 0.137 1401 Planarity : 0.003 0.040 1588 Dihedral : 4.493 57.090 1270 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.20 % Allowed : 19.80 % Favored : 76.00 % 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: 1.62 (0.25), residues: 1144 helix: 3.05 (0.24), residues: 461 sheet: 0.33 (0.34), residues: 217 loop : -0.63 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.001 PHE B 151 TYR 0.013 0.002 TYR R 242 ARG 0.008 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6388 (mmt180) REVERT: B 59 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7864 (t80) REVERT: B 85 TYR cc_start: 0.7344 (m-10) cc_final: 0.6968 (m-10) REVERT: B 155 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.7241 (t0) REVERT: B 215 GLU cc_start: 0.8178 (mp0) cc_final: 0.7815 (mt-10) REVERT: B 217 MET cc_start: 0.8557 (ppp) cc_final: 0.8229 (pp-130) REVERT: N 6 GLU cc_start: 0.6585 (mp0) cc_final: 0.6272 (mp0) REVERT: N 19 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6033 (ttm170) REVERT: R 338 ASN cc_start: 0.6022 (m-40) cc_final: 0.5682 (t0) REVERT: R 390 PHE cc_start: 0.7596 (t80) cc_final: 0.7283 (m-80) outliers start: 38 outliers final: 28 residues processed: 141 average time/residue: 1.3610 time to fit residues: 203.8925 Evaluate side-chains 154 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 56 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 0.0050 chunk 16 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN B 44 GLN B 175 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.188025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.131536 restraints weight = 10638.338| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.89 r_work: 0.3589 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9147 Z= 0.174 Angle : 0.470 6.278 12406 Z= 0.259 Chirality : 0.039 0.136 1401 Planarity : 0.003 0.040 1588 Dihedral : 4.436 57.718 1270 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.65 % Allowed : 20.13 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.26), residues: 1144 helix: 3.14 (0.24), residues: 461 sheet: 0.36 (0.34), residues: 217 loop : -0.63 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.012 0.001 TYR R 242 ARG 0.010 0.000 ARG A 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6974 (mtm110) cc_final: 0.6613 (mtp85) REVERT: B 42 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6386 (mmt180) REVERT: B 59 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7911 (t80) REVERT: B 85 TYR cc_start: 0.7339 (m-10) cc_final: 0.6963 (m-10) REVERT: B 155 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.7219 (t0) REVERT: B 175 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7568 (pp30) REVERT: B 215 GLU cc_start: 0.8186 (mp0) cc_final: 0.7824 (mt-10) REVERT: B 217 MET cc_start: 0.8568 (ppp) cc_final: 0.8244 (pp-130) REVERT: N 6 GLU cc_start: 0.6553 (mp0) cc_final: 0.6252 (mp0) REVERT: N 19 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.5988 (ttm170) REVERT: R 338 ASN cc_start: 0.5973 (m-40) cc_final: 0.5728 (t0) REVERT: R 390 PHE cc_start: 0.7582 (t80) cc_final: 0.7239 (m-80) outliers start: 33 outliers final: 27 residues processed: 138 average time/residue: 1.3770 time to fit residues: 202.5215 Evaluate side-chains 154 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 0.0470 chunk 69 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN B 44 GLN B 175 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN N 120 GLN ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.186662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129713 restraints weight = 10625.724| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.89 r_work: 0.3565 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9147 Z= 0.275 Angle : 0.540 6.626 12406 Z= 0.296 Chirality : 0.042 0.149 1401 Planarity : 0.004 0.040 1588 Dihedral : 4.719 58.129 1270 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.20 % Allowed : 19.58 % Favored : 76.22 % 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: 1.42 (0.25), residues: 1144 helix: 2.90 (0.24), residues: 455 sheet: 0.21 (0.34), residues: 218 loop : -0.68 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.011 0.002 HIS A 357 PHE 0.019 0.002 PHE B 151 TYR 0.016 0.002 TYR R 242 ARG 0.011 0.001 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13077.60 seconds wall clock time: 229 minutes 40.56 seconds (13780.56 seconds total)