Starting phenix.real_space_refine on Tue Mar 3 21:27:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rtb_24680/03_2026/7rtb_24680.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtb_24680/03_2026/7rtb_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_24680/03_2026/7rtb_24680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtb_24680/03_2026/7rtb_24680.map" model { file = "/net/cci-nas-00/data/ceres_data/7rtb_24680/03_2026/7rtb_24680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtb_24680/03_2026/7rtb_24680.cif" } resolution = 2.14 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'TRP:plan': 8, 'GLU:plan': 9, 'GLN:plan1': 8, 'ARG:plan': 7, 'TYR:plan': 5, 'ASP:plan': 8, 'PHE:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 2} 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: 2.11, per 1000 atoms: 0.23 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: 0.49 Conformation dependent library (CDL) restraints added in 292.0 milliseconds 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: 0.26 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: 1.31 Time building geometry restraints manager: 0.68 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: 3.280 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: 0.080 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.070 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:7.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.090 ------------------------------------------------------------------------------- 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 9150 Z= 0.206 Angle : 0.568 5.760 12412 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A 13 TYR 0.011 0.001 TYR P 13 PHE 0.009 0.001 PHE A 212 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9147) covalent geometry : angle 0.56783 (12406) SS BOND : bond 0.00103 ( 3) SS BOND : angle 0.29633 ( 6) hydrogen bonds : bond 0.15756 ( 472) hydrogen bonds : angle 6.08537 ( 1350) *********************** 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 : 0.360 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: 0.6411 time to fit residues: 111.3381 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 : 0.310 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.0070 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.2804 ------------------------------------------------------------------------------- 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 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 410 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.193058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.138022 restraints weight = 10655.804| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.91 r_work: 0.3659 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9150 Z= 0.114 Angle : 0.435 4.545 12412 Z= 0.242 Chirality : 0.038 0.127 1401 Planarity : 0.003 0.037 1588 Dihedral : 3.907 34.367 1273 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.54 % Allowed : 15.15 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.25), residues: 1144 helix: 2.04 (0.24), residues: 459 sheet: -0.00 (0.32), residues: 235 loop : -0.67 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 228 TYR 0.013 0.002 TYR P 13 PHE 0.013 0.001 PHE A 212 TRP 0.014 0.002 TRP B 82 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9147) covalent geometry : angle 0.43446 (12406) SS BOND : bond 0.00379 ( 3) SS BOND : angle 1.24291 ( 6) hydrogen bonds : bond 0.03965 ( 472) hydrogen bonds : angle 4.25752 ( 1350) *********************** 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 145 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6965 (mtm110) cc_final: 0.6647 (mtp85) REVERT: A 314 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6117 (mp0) REVERT: B 42 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6178 (mmt180) outliers start: 23 outliers final: 13 residues processed: 134 average time/residue: 0.6395 time to fit residues: 90.6605 Evaluate side-chains 130 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 175 GLN Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 146 ILE 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 386 THR Chi-restraints excluded: chain R residue 390 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 36 optimal weight: 0.0770 chunk 84 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 72 optimal weight: 0.0870 chunk 39 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 chunk 105 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 292 ASN B 44 GLN B 175 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN N 35 ASN N 39 GLN N 77 ASN N 120 GLN ** R 221 GLN ** 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 = 0.4450 r_free = 0.4450 target = 0.194084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.139429 restraints weight = 10617.789| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.89 r_work: 0.3683 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.036 9150 Z= 0.073 Angle : 0.369 5.217 12412 Z= 0.207 Chirality : 0.036 0.127 1401 Planarity : 0.002 0.032 1588 Dihedral : 3.510 29.119 1270 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.10 % Allowed : 15.71 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.25), residues: 1144 helix: 2.74 (0.25), residues: 460 sheet: 0.25 (0.33), residues: 222 loop : -0.45 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.009 0.001 TYR A 339 PHE 0.008 0.001 PHE A 212 TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00145 ( 9147) covalent geometry : angle 0.36908 (12406) SS BOND : bond 0.00291 ( 3) SS BOND : angle 0.65152 ( 6) hydrogen bonds : bond 0.03130 ( 472) hydrogen bonds : angle 3.85437 ( 1350) *********************** 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 150 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.286 Fit side-chains REVERT: A 20 ARG cc_start: 0.6921 (mtm110) cc_final: 0.6618 (mtp85) REVERT: A 314 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6114 (mp0) REVERT: B 42 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6122 (mmt180) REVERT: B 217 MET cc_start: 0.8520 (ppp) cc_final: 0.8271 (pp-130) REVERT: N 34 MET cc_start: 0.7889 (mmm) cc_final: 0.7361 (mmm) REVERT: R 338 ASN cc_start: 0.5463 (m-40) cc_final: 0.5061 (t0) REVERT: R 362 THR cc_start: 0.7687 (OUTLIER) cc_final: 0.7282 (p) outliers start: 28 outliers final: 16 residues processed: 135 average time/residue: 0.6416 time to fit residues: 91.7197 Evaluate side-chains 134 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 291 LEU 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 B residue 340 ASN 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 R residue 146 ILE Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 287 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 50.0000 chunk 93 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 76 optimal weight: 0.0010 chunk 89 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 267 GLN A 292 ASN B 44 GLN B 175 GLN B 268 ASN N 77 ASN N 120 GLN R 221 GLN R 304 ASN R 410 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.193577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.138250 restraints weight = 10742.761| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.92 r_work: 0.3681 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.019 9150 Z= 0.068 Angle : 0.359 3.854 12412 Z= 0.200 Chirality : 0.036 0.127 1401 Planarity : 0.002 0.028 1588 Dihedral : 3.381 23.928 1270 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.32 % Allowed : 16.59 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.26), residues: 1144 helix: 3.14 (0.24), residues: 460 sheet: 0.37 (0.33), residues: 217 loop : -0.32 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.011 0.001 TYR R 305 PHE 0.008 0.001 PHE A 212 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00133 ( 9147) covalent geometry : angle 0.35852 (12406) SS BOND : bond 0.00208 ( 3) SS BOND : angle 0.39452 ( 6) hydrogen bonds : bond 0.02920 ( 472) hydrogen bonds : angle 3.69589 ( 1350) *********************** 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 148 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.341 Fit side-chains REVERT: A 314 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6311 (mt-10) REVERT: B 42 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6079 (mmt180) REVERT: B 85 TYR cc_start: 0.7172 (m-10) cc_final: 0.6728 (m-10) REVERT: B 197 ARG cc_start: 0.7046 (mmm-85) cc_final: 0.6648 (mmp-170) REVERT: B 217 MET cc_start: 0.8558 (ppp) cc_final: 0.8279 (pp-130) REVERT: R 338 ASN cc_start: 0.5483 (m-40) cc_final: 0.5152 (t0) outliers start: 30 outliers final: 15 residues processed: 132 average time/residue: 0.6577 time to fit residues: 92.2324 Evaluate side-chains 131 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 22 CYS 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 287 VAL Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 343 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 68 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 62 optimal weight: 0.0000 chunk 13 optimal weight: 4.9990 chunk 65 optimal weight: 0.0040 chunk 70 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 292 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 176 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 77 ASN N 120 GLN R 221 GLN R 304 ASN R 410 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.192512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.136837 restraints weight = 10633.239| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.91 r_work: 0.3662 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 9150 Z= 0.079 Angle : 0.376 3.803 12412 Z= 0.209 Chirality : 0.037 0.128 1401 Planarity : 0.002 0.028 1588 Dihedral : 3.424 23.010 1269 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.32 % Allowed : 17.04 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.26), residues: 1144 helix: 3.34 (0.24), residues: 460 sheet: 0.33 (0.33), residues: 223 loop : -0.23 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.012 0.001 TYR R 305 PHE 0.009 0.001 PHE A 212 TRP 0.014 0.001 TRP R 203 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00158 ( 9147) covalent geometry : angle 0.37620 (12406) SS BOND : bond 0.00270 ( 3) SS BOND : angle 0.57800 ( 6) hydrogen bonds : bond 0.03054 ( 472) hydrogen bonds : angle 3.70989 ( 1350) *********************** 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 149 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.324 Fit side-chains REVERT: A 314 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6148 (mp0) REVERT: B 42 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6095 (mmt180) REVERT: B 85 TYR cc_start: 0.7213 (m-10) cc_final: 0.6760 (m-10) REVERT: B 217 MET cc_start: 0.8588 (ppp) cc_final: 0.8318 (pp-130) REVERT: R 338 ASN cc_start: 0.5621 (m-40) cc_final: 0.5147 (t0) outliers start: 30 outliers final: 20 residues processed: 134 average time/residue: 0.5845 time to fit residues: 83.2675 Evaluate side-chains 138 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 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 277 SER Chi-restraints excluded: chain G residue 21 MET 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 149 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 272 ILE 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 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 97 optimal weight: 3.9990 chunk 16 optimal weight: 0.0470 chunk 11 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 44 GLN B 110 ASN B 175 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 77 ASN N 120 GLN R 304 ASN R 410 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.187518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.130420 restraints weight = 10583.227| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.91 r_work: 0.3575 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9150 Z= 0.208 Angle : 0.564 7.311 12412 Z= 0.310 Chirality : 0.043 0.145 1401 Planarity : 0.005 0.040 1588 Dihedral : 4.381 22.678 1269 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.65 % Allowed : 18.25 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.25), residues: 1144 helix: 2.77 (0.24), residues: 459 sheet: 0.31 (0.33), residues: 218 loop : -0.54 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 20 TYR 0.015 0.002 TYR R 242 PHE 0.017 0.002 PHE R 280 TRP 0.021 0.002 TRP A 234 HIS 0.010 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 9147) covalent geometry : angle 0.56383 (12406) SS BOND : bond 0.00589 ( 3) SS BOND : angle 1.21765 ( 6) hydrogen bonds : bond 0.04507 ( 472) hydrogen bonds : angle 4.44517 ( 1350) *********************** 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 157 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.252 Fit side-chains REVERT: A 20 ARG cc_start: 0.7019 (mtm110) cc_final: 0.6805 (mmt180) REVERT: B 42 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6338 (mmt180) REVERT: B 85 TYR cc_start: 0.7332 (m-10) cc_final: 0.6889 (m-10) REVERT: R 338 ASN cc_start: 0.5830 (m-40) cc_final: 0.5521 (t0) outliers start: 33 outliers final: 21 residues processed: 138 average time/residue: 0.6094 time to fit residues: 88.9385 Evaluate side-chains 136 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 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 B residue 277 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.0020 chunk 45 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN 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 304 ASN R 410 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.190645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.134680 restraints weight = 10621.039| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.89 r_work: 0.3635 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9150 Z= 0.081 Angle : 0.395 5.096 12412 Z= 0.220 Chirality : 0.037 0.130 1401 Planarity : 0.002 0.032 1588 Dihedral : 3.687 20.572 1269 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.32 % Allowed : 20.24 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.26), residues: 1144 helix: 3.37 (0.24), residues: 464 sheet: 0.53 (0.34), residues: 216 loop : -0.48 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.014 0.001 TYR R 305 PHE 0.009 0.001 PHE B 151 TRP 0.017 0.001 TRP R 203 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00161 ( 9147) covalent geometry : angle 0.39402 (12406) SS BOND : bond 0.00512 ( 3) SS BOND : angle 1.19741 ( 6) hydrogen bonds : bond 0.03195 ( 472) hydrogen bonds : angle 3.88450 ( 1350) *********************** 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 142 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.354 Fit side-chains REVERT: A 314 GLU cc_start: 0.6763 (tm-30) cc_final: 0.6350 (mp0) REVERT: B 42 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6225 (mmt180) REVERT: B 59 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7764 (t80) REVERT: B 85 TYR cc_start: 0.7271 (m-10) cc_final: 0.6844 (m-10) REVERT: R 338 ASN cc_start: 0.5586 (m-40) cc_final: 0.5349 (t0) outliers start: 21 outliers final: 13 residues processed: 131 average time/residue: 0.5982 time to fit residues: 83.1215 Evaluate side-chains 129 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 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 G residue 21 MET Chi-restraints excluded: chain N residue 22 CYS 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 390 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 29 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 81 optimal weight: 0.0050 chunk 53 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN 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 304 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.191263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.135262 restraints weight = 10558.481| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.90 r_work: 0.3640 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9150 Z= 0.077 Angle : 0.393 4.430 12412 Z= 0.217 Chirality : 0.037 0.129 1401 Planarity : 0.002 0.032 1588 Dihedral : 3.582 20.349 1269 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.77 % Allowed : 20.24 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.26), residues: 1144 helix: 3.55 (0.24), residues: 464 sheet: 0.51 (0.33), residues: 223 loop : -0.40 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 20 TYR 0.013 0.001 TYR R 305 PHE 0.009 0.001 PHE B 151 TRP 0.015 0.001 TRP R 203 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00156 ( 9147) covalent geometry : angle 0.39083 (12406) SS BOND : bond 0.00318 ( 3) SS BOND : angle 1.95721 ( 6) hydrogen bonds : bond 0.03095 ( 472) hydrogen bonds : angle 3.76816 ( 1350) *********************** 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 144 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.316 Fit side-chains REVERT: A 314 GLU cc_start: 0.6768 (tm-30) cc_final: 0.6349 (mp0) REVERT: B 42 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6220 (mmt180) REVERT: B 59 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7777 (t80) REVERT: B 85 TYR cc_start: 0.7268 (m-10) cc_final: 0.6822 (m-10) REVERT: B 155 ASN cc_start: 0.7364 (OUTLIER) cc_final: 0.6986 (t0) outliers start: 25 outliers final: 12 residues processed: 132 average time/residue: 0.6174 time to fit residues: 86.3708 Evaluate side-chains 130 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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 177 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 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 386 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 19 optimal weight: 0.0270 chunk 27 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 73 optimal weight: 30.0000 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- 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 R 304 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.189683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133183 restraints weight = 10564.194| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.90 r_work: 0.3609 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9150 Z= 0.113 Angle : 0.438 5.272 12412 Z= 0.241 Chirality : 0.038 0.132 1401 Planarity : 0.003 0.031 1588 Dihedral : 3.830 20.597 1269 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.88 % Allowed : 20.02 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.26), residues: 1144 helix: 3.47 (0.24), residues: 461 sheet: 0.52 (0.34), residues: 217 loop : -0.32 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 20 TYR 0.012 0.001 TYR R 242 PHE 0.012 0.001 PHE B 151 TRP 0.019 0.001 TRP R 203 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9147) covalent geometry : angle 0.43686 (12406) SS BOND : bond 0.00409 ( 3) SS BOND : angle 1.43325 ( 6) hydrogen bonds : bond 0.03494 ( 472) hydrogen bonds : angle 3.95636 ( 1350) *********************** 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 144 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.335 Fit side-chains REVERT: A 20 ARG cc_start: 0.6914 (mtm110) cc_final: 0.6379 (mtp85) REVERT: A 314 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6331 (mp0) REVERT: B 42 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6277 (mmt180) REVERT: B 85 TYR cc_start: 0.7278 (m-10) cc_final: 0.6836 (m-10) REVERT: B 155 ASN cc_start: 0.7407 (OUTLIER) cc_final: 0.7003 (t0) REVERT: R 362 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7710 (p) outliers start: 26 outliers final: 20 residues processed: 133 average time/residue: 0.5708 time to fit residues: 80.6594 Evaluate side-chains 138 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 334 VAL 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 277 SER 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 149 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 287 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 110 optimal weight: 0.0040 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 overall best weight: 1.0006 ------------------------------------------------------------------------------- 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 R 304 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.190157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.133863 restraints weight = 10620.996| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.89 r_work: 0.3620 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9150 Z= 0.093 Angle : 0.417 5.769 12412 Z= 0.229 Chirality : 0.038 0.131 1401 Planarity : 0.003 0.032 1588 Dihedral : 3.735 20.368 1269 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.65 % Allowed : 20.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.26), residues: 1144 helix: 3.55 (0.24), residues: 461 sheet: 0.55 (0.33), residues: 221 loop : -0.26 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 20 TYR 0.011 0.001 TYR R 305 PHE 0.011 0.001 PHE B 151 TRP 0.020 0.001 TRP R 203 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 9147) covalent geometry : angle 0.41586 (12406) SS BOND : bond 0.00329 ( 3) SS BOND : angle 1.13544 ( 6) hydrogen bonds : bond 0.03305 ( 472) hydrogen bonds : angle 3.88428 ( 1350) ********************** 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 138 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.388 Fit side-chains REVERT: A 314 GLU cc_start: 0.6853 (tm-30) cc_final: 0.6312 (mp0) REVERT: B 42 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6273 (mmt180) REVERT: B 59 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7734 (t80) REVERT: B 85 TYR cc_start: 0.7263 (m-10) cc_final: 0.6820 (m-10) REVERT: B 155 ASN cc_start: 0.7388 (OUTLIER) cc_final: 0.6982 (t0) REVERT: R 362 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7696 (p) outliers start: 24 outliers final: 18 residues processed: 127 average time/residue: 0.6323 time to fit residues: 85.1842 Evaluate side-chains 135 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 334 VAL 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 277 SER 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 83 MET Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 287 VAL 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 65 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 chunk 5 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 R 304 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.189766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133372 restraints weight = 10431.691| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.88 r_work: 0.3615 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9150 Z= 0.109 Angle : 0.433 5.745 12412 Z= 0.237 Chirality : 0.038 0.131 1401 Planarity : 0.003 0.035 1588 Dihedral : 3.788 20.525 1269 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.77 % Allowed : 20.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.26), residues: 1144 helix: 3.48 (0.24), residues: 464 sheet: 0.60 (0.34), residues: 216 loop : -0.33 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 20 TYR 0.011 0.001 TYR R 305 PHE 0.013 0.001 PHE B 151 TRP 0.019 0.001 TRP R 203 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9147) covalent geometry : angle 0.43217 (12406) SS BOND : bond 0.00407 ( 3) SS BOND : angle 1.22156 ( 6) hydrogen bonds : bond 0.03423 ( 472) hydrogen bonds : angle 3.92758 ( 1350) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6351.19 seconds wall clock time: 108 minutes 8.71 seconds (6488.71 seconds total)