Starting phenix.real_space_refine on Mon Jul 28 16:33:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kdi_37137/07_2025/8kdi_37137.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kdi_37137/07_2025/8kdi_37137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kdi_37137/07_2025/8kdi_37137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kdi_37137/07_2025/8kdi_37137.map" model { file = "/net/cci-nas-00/data/ceres_data/8kdi_37137/07_2025/8kdi_37137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kdi_37137/07_2025/8kdi_37137.cif" } resolution = 3.58 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 6811 2.51 5 N 1718 2.21 5 O 1963 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10532 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3650 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain: "B" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3451 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 23, 'TRANS': 423} Chain breaks: 1 Chain: "L" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1686 Classifications: {'peptide': 217} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 205} Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1689 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.40, per 1000 atoms: 0.61 Number of scatterers: 10532 At special positions: 0 Unit cell: (81.3285, 141.174, 148.847, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1963 8.00 N 1718 7.00 C 6811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS B 164 " distance=2.12 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.12 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.11 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 202 " distance=2.07 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 381 " " NAG A 702 " - " ASN A 506 " " NAG A 703 " - " ASN A 365 " " NAG A 704 " - " ASN A 424 " Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.5 seconds 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2502 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 47.4% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 165 through 173 removed outlier: 5.341A pdb=" N LYS A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 207 Processing helix chain 'A' and resid 217 through 222 removed outlier: 4.170A pdb=" N GLY A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.750A pdb=" N GLY A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ASP A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 322 through 341 removed outlier: 3.641A pdb=" N VAL A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 355 through 371 Processing helix chain 'A' and resid 384 through 395 removed outlier: 4.256A pdb=" N SER A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASN A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 4.270A pdb=" N ASP A 407 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 504 through 507 Processing helix chain 'A' and resid 508 through 514 removed outlier: 4.039A pdb=" N GLU A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 533 Processing helix chain 'A' and resid 533 through 539 Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.508A pdb=" N ALA B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 71 through 80 Processing helix chain 'B' and resid 81 through 110 removed outlier: 3.585A pdb=" N ALA B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.853A pdb=" N TYR B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 139 removed outlier: 3.599A pdb=" N PHE B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 158 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 167 through 189 removed outlier: 3.757A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 222 removed outlier: 4.267A pdb=" N ARG B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALA B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 254 removed outlier: 3.527A pdb=" N LEU B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 removed outlier: 3.688A pdb=" N LEU B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN B 261 " --> pdb=" O TRP B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 261' Processing helix chain 'B' and resid 262 through 267 Processing helix chain 'B' and resid 272 through 298 removed outlier: 3.746A pdb=" N LEU B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 310 through 320 removed outlier: 3.711A pdb=" N ASP B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 325 Processing helix chain 'B' and resid 326 through 345 Processing helix chain 'B' and resid 346 through 356 removed outlier: 3.914A pdb=" N PHE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 365 Processing helix chain 'B' and resid 373 through 387 removed outlier: 3.869A pdb=" N TYR B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 392 through 422 Processing helix chain 'B' and resid 435 through 454 removed outlier: 4.332A pdb=" N LEU B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TRP B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.770A pdb=" N CYS B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 476 removed outlier: 4.304A pdb=" N VAL B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 501 Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.917A pdb=" N LEU L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 133 Processing helix chain 'L' and resid 189 through 194 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.744A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.536A pdb=" N LYS H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 136 through 140 removed outlier: 3.930A pdb=" N ASN H 140 " --> pdb=" O ALA H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 198 removed outlier: 3.598A pdb=" N GLU H 198 " --> pdb=" O TRP H 195 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 399 through 401 removed outlier: 3.649A pdb=" N LEU A 399 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE A 345 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLY A 379 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL A 347 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 466 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 540 through 544 removed outlier: 4.042A pdb=" N SER A 552 " --> pdb=" O PHE A 544 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU A 595 " --> pdb=" O ARG A 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 574 removed outlier: 6.362A pdb=" N GLY A 573 " --> pdb=" O ILE L 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 14 removed outlier: 3.672A pdb=" N ALA L 90 " --> pdb=" O LEU L 110 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 14 removed outlier: 3.672A pdb=" N ALA L 90 " --> pdb=" O LEU L 110 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR L 103 " --> pdb=" O GLN L 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 120 through 124 removed outlier: 3.620A pdb=" N VAL L 139 " --> pdb=" O PHE L 124 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR L 179 " --> pdb=" O ASN L 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 159 through 161 removed outlier: 4.430A pdb=" N TRP L 154 " --> pdb=" O ARG L 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.477A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.477A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 127 through 131 removed outlier: 5.329A pdb=" N THR H 144 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL H 190 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLY H 146 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL H 188 " --> pdb=" O GLY H 146 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU H 148 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER H 186 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LYS H 150 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU H 184 " --> pdb=" O LYS H 150 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N SER H 185 " --> pdb=" O PRO H 174 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER H 187 " --> pdb=" O THR H 172 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N THR H 172 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THR H 189 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL H 170 " --> pdb=" O THR H 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 201 through 205 removed outlier: 3.584A pdb=" N LYS H 215 " --> pdb=" O CYS H 202 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1482 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: 3.72 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1698 1.31 - 1.44: 3022 1.44 - 1.58: 6015 1.58 - 1.72: 4 1.72 - 1.85: 58 Bond restraints: 10797 Sorted by residual: bond pdb=" CG HIS L 97 " pdb=" CD2 HIS L 97 " ideal model delta sigma weight residual 1.354 1.251 0.103 1.10e-02 8.26e+03 8.68e+01 bond pdb=" CB HIS L 97 " pdb=" CG HIS L 97 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.68e+01 bond pdb=" CB HIS H 35 " pdb=" CG HIS H 35 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.43e+01 bond pdb=" C GLY A 462 " pdb=" O GLY A 462 " ideal model delta sigma weight residual 1.229 1.190 0.040 8.20e-03 1.49e+04 2.33e+01 bond pdb=" C LEU A 213 " pdb=" N PRO A 214 " ideal model delta sigma weight residual 1.331 1.269 0.061 1.31e-02 5.83e+03 2.18e+01 ... (remaining 10792 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 14204 4.37 - 8.74: 483 8.74 - 13.11: 25 13.11 - 17.48: 1 17.48 - 21.85: 1 Bond angle restraints: 14714 Sorted by residual: angle pdb=" O LEU A 213 " pdb=" C LEU A 213 " pdb=" N PRO A 214 " ideal model delta sigma weight residual 121.42 99.57 21.85 1.06e+00 8.90e-01 4.25e+02 angle pdb=" CA LEU A 213 " pdb=" C LEU A 213 " pdb=" O LEU A 213 " ideal model delta sigma weight residual 119.76 132.87 -13.11 8.90e-01 1.26e+00 2.17e+02 angle pdb=" C LEU A 213 " pdb=" N PRO A 214 " pdb=" CA PRO A 214 " ideal model delta sigma weight residual 119.85 111.75 8.10 1.01e+00 9.80e-01 6.43e+01 angle pdb=" N PRO A 214 " pdb=" CA PRO A 214 " pdb=" CB PRO A 214 " ideal model delta sigma weight residual 103.33 95.93 7.40 9.30e-01 1.16e+00 6.34e+01 angle pdb=" CA LEU A 213 " pdb=" C LEU A 213 " pdb=" N PRO A 214 " ideal model delta sigma weight residual 118.75 126.47 -7.72 9.70e-01 1.06e+00 6.33e+01 ... (remaining 14709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 5867 17.57 - 35.14: 434 35.14 - 52.72: 87 52.72 - 70.29: 13 70.29 - 87.86: 11 Dihedral angle restraints: 6412 sinusoidal: 2513 harmonic: 3899 Sorted by residual: dihedral pdb=" CA SER A 410 " pdb=" C SER A 410 " pdb=" N THR A 411 " pdb=" CA THR A 411 " ideal model delta harmonic sigma weight residual 180.00 136.43 43.57 0 5.00e+00 4.00e-02 7.59e+01 dihedral pdb=" CA TRP A 557 " pdb=" C TRP A 557 " pdb=" N ASP A 558 " pdb=" CA ASP A 558 " ideal model delta harmonic sigma weight residual -180.00 -148.80 -31.20 0 5.00e+00 4.00e-02 3.89e+01 dihedral pdb=" CA GLY A 412 " pdb=" C GLY A 412 " pdb=" N GLU A 413 " pdb=" CA GLU A 413 " ideal model delta harmonic sigma weight residual 180.00 -149.09 -30.91 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 6409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1368 0.117 - 0.233: 312 0.233 - 0.349: 16 0.349 - 0.466: 3 0.466 - 0.582: 1 Chirality restraints: 1700 Sorted by residual: chirality pdb=" CA PRO A 548 " pdb=" N PRO A 548 " pdb=" C PRO A 548 " pdb=" CB PRO A 548 " both_signs ideal model delta sigma weight residual False 2.72 2.14 0.58 2.00e-01 2.50e+01 8.47e+00 chirality pdb=" CA HIS L 97 " pdb=" N HIS L 97 " pdb=" C HIS L 97 " pdb=" CB HIS L 97 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.05e+00 chirality pdb=" CA TYR H 103 " pdb=" N TYR H 103 " pdb=" C TYR H 103 " pdb=" CB TYR H 103 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 1697 not shown) Planarity restraints: 1845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 702 " -0.088 2.00e-02 2.50e+03 7.34e-02 6.74e+01 pdb=" C7 NAG A 702 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG A 702 " -0.067 2.00e-02 2.50e+03 pdb=" N2 NAG A 702 " 0.118 2.00e-02 2.50e+03 pdb=" O7 NAG A 702 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 100 " -0.509 9.50e-02 1.11e+02 2.28e-01 3.21e+01 pdb=" NE ARG H 100 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG H 100 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG H 100 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG H 100 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 525 " 0.387 9.50e-02 1.11e+02 1.73e-01 1.86e+01 pdb=" NE ARG A 525 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 525 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 525 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 525 " 0.017 2.00e-02 2.50e+03 ... (remaining 1842 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 20 2.60 - 3.17: 8927 3.17 - 3.75: 15713 3.75 - 4.32: 22987 4.32 - 4.90: 37298 Nonbonded interactions: 84945 Sorted by model distance: nonbonded pdb=" O LEU A 213 " pdb=" CA PRO A 214 " model vdw 2.022 2.776 nonbonded pdb=" CB LYS A 532 " pdb=" OE1 GLU B 303 " model vdw 2.074 3.440 nonbonded pdb=" OH TYR A 250 " pdb=" OE2 GLU A 471 " model vdw 2.309 3.040 nonbonded pdb=" O LEU A 213 " pdb=" C PRO A 214 " model vdw 2.334 3.270 nonbonded pdb=" CB GLN L 96 " pdb=" OE1 GLN L 96 " model vdw 2.497 2.752 ... (remaining 84940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.450 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 : 0.013 0.103 10806 Z= 0.822 Angle : 1.930 21.854 14736 Z= 1.271 Chirality : 0.092 0.582 1700 Planarity : 0.012 0.228 1841 Dihedral : 13.638 87.859 3895 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.54 % Favored : 95.38 % Rotamer: Outliers : 1.47 % Allowed : 5.11 % Favored : 93.42 % Cbeta Deviations : 0.72 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.92 (0.20), residues: 1343 helix: -1.68 (0.18), residues: 509 sheet: -0.34 (0.30), residues: 270 loop : -1.16 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.007 TRP H 110 HIS 0.010 0.003 HIS A 619 PHE 0.029 0.005 PHE L 56 TYR 0.029 0.005 TYR A 250 ARG 0.009 0.002 ARG A 562 Details of bonding type rmsd link_NAG-ASN : bond 0.01216 ( 4) link_NAG-ASN : angle 4.84201 ( 12) hydrogen bonds : bond 0.18393 ( 535) hydrogen bonds : angle 8.28512 ( 1482) SS BOND : bond 0.06864 ( 5) SS BOND : angle 4.60584 ( 10) covalent geometry : bond 0.01297 (10797) covalent geometry : angle 1.92294 (14714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 290 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ARG cc_start: 0.4716 (mtm110) cc_final: 0.4196 (mtm180) REVERT: A 211 ARG cc_start: 0.6786 (ttm-80) cc_final: 0.6397 (ttt180) REVERT: A 212 GLU cc_start: 0.8021 (pm20) cc_final: 0.7666 (tt0) REVERT: A 234 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7197 (mt0) REVERT: A 236 HIS cc_start: 0.6447 (m-70) cc_final: 0.5929 (m-70) REVERT: A 252 SER cc_start: 0.8897 (t) cc_final: 0.8662 (p) REVERT: A 290 PHE cc_start: 0.8210 (t80) cc_final: 0.7911 (t80) REVERT: A 442 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8677 (p) REVERT: A 457 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8735 (mt) REVERT: A 475 ASP cc_start: 0.8306 (t0) cc_final: 0.7896 (p0) REVERT: A 484 MET cc_start: 0.8558 (mtm) cc_final: 0.8055 (tpt) REVERT: A 535 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.7879 (t) REVERT: A 604 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8181 (pm20) REVERT: A 612 GLU cc_start: 0.8156 (tt0) cc_final: 0.7838 (tp30) REVERT: A 625 ARG cc_start: 0.8135 (ttt90) cc_final: 0.7879 (ttp80) REVERT: B 81 SER cc_start: 0.8610 (t) cc_final: 0.8350 (p) REVERT: B 242 ASN cc_start: 0.6538 (m110) cc_final: 0.6177 (p0) REVERT: B 265 GLU cc_start: 0.5906 (tm-30) cc_final: 0.5617 (tp30) REVERT: B 268 ILE cc_start: 0.5238 (mm) cc_final: 0.4827 (tt) REVERT: B 296 TYR cc_start: 0.7016 (m-80) cc_final: 0.6718 (m-10) REVERT: B 349 LEU cc_start: 0.8726 (tp) cc_final: 0.8496 (tt) REVERT: B 365 MET cc_start: 0.8348 (mtt) cc_final: 0.7948 (mmm) REVERT: B 387 TYR cc_start: 0.7809 (m-80) cc_final: 0.7481 (m-80) REVERT: B 444 LEU cc_start: 0.8718 (mt) cc_final: 0.8494 (tp) REVERT: B 454 THR cc_start: 0.8275 (p) cc_final: 0.7898 (t) REVERT: L 1 ASP cc_start: 0.7532 (m-30) cc_final: 0.6981 (p0) REVERT: L 21 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7257 (mmt) REVERT: L 66 ASP cc_start: 0.8502 (m-30) cc_final: 0.8131 (t0) REVERT: L 111 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7619 (mm-30) REVERT: L 124 PHE cc_start: 0.8587 (m-80) cc_final: 0.8157 (m-80) REVERT: L 130 GLN cc_start: 0.9009 (tt0) cc_final: 0.8737 (tm-30) REVERT: L 154 TRP cc_start: 0.8374 (m100) cc_final: 0.7891 (m100) REVERT: H 6 GLN cc_start: 0.8811 (mt0) cc_final: 0.8501 (mt0) REVERT: H 10 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7624 (mm-30) REVERT: H 112 GLN cc_start: 0.8504 (mm-40) cc_final: 0.7994 (pm20) REVERT: H 178 GLN cc_start: 0.7005 (mm-40) cc_final: 0.6804 (pt0) REVERT: H 180 ASP cc_start: 0.8655 (m-30) cc_final: 0.8294 (p0) outliers start: 17 outliers final: 3 residues processed: 302 average time/residue: 0.2614 time to fit residues: 107.5377 Evaluate side-chains 186 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 179 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain H residue 83 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 339 GLN A 352 ASN B 358 HIS ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 172 GLN H 140 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.156500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118019 restraints weight = 14794.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.107009 restraints weight = 22072.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.104386 restraints weight = 24669.897| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10806 Z= 0.153 Angle : 0.729 7.760 14736 Z= 0.372 Chirality : 0.046 0.202 1700 Planarity : 0.005 0.036 1841 Dihedral : 7.090 53.708 1536 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.86 % Allowed : 12.12 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.21 (0.22), residues: 1343 helix: 0.81 (0.22), residues: 516 sheet: 0.21 (0.31), residues: 271 loop : -0.40 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 HIS 0.005 0.001 HIS B 367 PHE 0.026 0.002 PHE B 403 TYR 0.034 0.002 TYR H 103 ARG 0.006 0.001 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 4) link_NAG-ASN : angle 2.51941 ( 12) hydrogen bonds : bond 0.04762 ( 535) hydrogen bonds : angle 5.19294 ( 1482) SS BOND : bond 0.00436 ( 5) SS BOND : angle 1.65184 ( 10) covalent geometry : bond 0.00326 (10797) covalent geometry : angle 0.72510 (14714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.8951 (p) REVERT: A 528 ASP cc_start: 0.7751 (t0) cc_final: 0.7475 (t0) REVERT: A 594 ASP cc_start: 0.7022 (m-30) cc_final: 0.6788 (m-30) REVERT: B 294 LEU cc_start: 0.8247 (tp) cc_final: 0.7869 (tp) REVERT: B 369 GLN cc_start: 0.7622 (mp10) cc_final: 0.7196 (tm-30) REVERT: B 387 TYR cc_start: 0.8793 (m-80) cc_final: 0.8291 (m-80) REVERT: B 391 LYS cc_start: 0.7957 (mmpt) cc_final: 0.7108 (ptpp) REVERT: B 441 LEU cc_start: 0.7075 (mm) cc_final: 0.6813 (pp) REVERT: B 454 THR cc_start: 0.7054 (p) cc_final: 0.6564 (t) REVERT: L 129 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8017 (mt-10) REVERT: L 154 TRP cc_start: 0.8564 (m100) cc_final: 0.8139 (m100) REVERT: H 198 GLU cc_start: 0.7799 (mp0) cc_final: 0.7430 (mp0) outliers start: 33 outliers final: 19 residues processed: 218 average time/residue: 0.2630 time to fit residues: 79.7019 Evaluate side-chains 162 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 204 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 104 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 116 optimal weight: 0.2980 chunk 98 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 45 optimal weight: 0.0050 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** L 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN H 6 GLN H 19 ASN H 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.161165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126100 restraints weight = 14976.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.125612 restraints weight = 21803.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.119675 restraints weight = 20593.976| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10806 Z= 0.170 Angle : 0.678 7.219 14736 Z= 0.343 Chirality : 0.044 0.191 1700 Planarity : 0.004 0.037 1841 Dihedral : 6.097 55.734 1528 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.42 % Allowed : 14.98 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.63 (0.23), residues: 1343 helix: 1.27 (0.22), residues: 522 sheet: 0.40 (0.31), residues: 273 loop : -0.30 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 HIS 0.008 0.001 HIS B 358 PHE 0.026 0.002 PHE B 95 TYR 0.033 0.002 TYR H 103 ARG 0.004 0.001 ARG A 613 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 4) link_NAG-ASN : angle 2.13340 ( 12) hydrogen bonds : bond 0.04326 ( 535) hydrogen bonds : angle 4.79769 ( 1482) SS BOND : bond 0.00409 ( 5) SS BOND : angle 1.35674 ( 10) covalent geometry : bond 0.00383 (10797) covalent geometry : angle 0.67512 (14714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 ASP cc_start: 0.7533 (t0) cc_final: 0.7313 (t0) REVERT: B 145 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7985 (mp10) REVERT: B 294 LEU cc_start: 0.7680 (tp) cc_final: 0.7376 (tp) REVERT: B 387 TYR cc_start: 0.8742 (m-80) cc_final: 0.8407 (m-80) REVERT: B 391 LYS cc_start: 0.7602 (mmpt) cc_final: 0.6971 (ptpp) REVERT: B 454 THR cc_start: 0.6580 (p) cc_final: 0.6275 (t) REVERT: L 189 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7340 (tptm) REVERT: H 73 ASP cc_start: 0.7117 (t0) cc_final: 0.6817 (t70) REVERT: H 89 GLU cc_start: 0.7007 (tt0) cc_final: 0.6479 (tt0) REVERT: H 129 TYR cc_start: 0.7901 (m-80) cc_final: 0.7502 (m-80) outliers start: 28 outliers final: 16 residues processed: 174 average time/residue: 0.2225 time to fit residues: 55.1740 Evaluate side-chains 149 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 431 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 159 SER Chi-restraints excluded: chain L residue 189 LYS Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 204 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 101 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 52 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 95 optimal weight: 0.0970 chunk 40 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.161809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128000 restraints weight = 14692.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127327 restraints weight = 23192.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126754 restraints weight = 22011.205| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10806 Z= 0.141 Angle : 0.642 8.631 14736 Z= 0.322 Chirality : 0.043 0.201 1700 Planarity : 0.004 0.044 1841 Dihedral : 5.575 55.157 1525 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.03 % Allowed : 15.24 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.83 (0.23), residues: 1343 helix: 1.53 (0.23), residues: 524 sheet: 0.46 (0.31), residues: 281 loop : -0.30 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 47 HIS 0.005 0.001 HIS L 97 PHE 0.022 0.002 PHE B 445 TYR 0.032 0.001 TYR H 103 ARG 0.004 0.000 ARG L 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 4) link_NAG-ASN : angle 1.68767 ( 12) hydrogen bonds : bond 0.03957 ( 535) hydrogen bonds : angle 4.60013 ( 1482) SS BOND : bond 0.00327 ( 5) SS BOND : angle 1.10033 ( 10) covalent geometry : bond 0.00319 (10797) covalent geometry : angle 0.64024 (14714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 ASP cc_start: 0.7867 (t0) cc_final: 0.7635 (t0) REVERT: A 528 ASP cc_start: 0.7689 (t0) cc_final: 0.7476 (t0) REVERT: B 294 LEU cc_start: 0.7651 (tp) cc_final: 0.7402 (tp) REVERT: B 369 GLN cc_start: 0.6637 (tp40) cc_final: 0.6073 (tm-30) REVERT: B 387 TYR cc_start: 0.8765 (m-80) cc_final: 0.8556 (m-80) REVERT: B 391 LYS cc_start: 0.7850 (mmpt) cc_final: 0.7113 (ptpp) REVERT: B 454 THR cc_start: 0.6429 (p) cc_final: 0.6200 (t) REVERT: L 189 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7748 (tptm) REVERT: H 73 ASP cc_start: 0.7289 (t0) cc_final: 0.6863 (t70) outliers start: 35 outliers final: 21 residues processed: 169 average time/residue: 0.2207 time to fit residues: 53.5039 Evaluate side-chains 143 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 431 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 189 LYS Chi-restraints excluded: chain L residue 211 ILE Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 204 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 88 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 57 optimal weight: 0.0040 chunk 101 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN L 43 GLN H 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.161915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127174 restraints weight = 14868.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126734 restraints weight = 22070.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.117209 restraints weight = 20325.237| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10806 Z= 0.128 Angle : 0.636 8.883 14736 Z= 0.315 Chirality : 0.042 0.191 1700 Planarity : 0.004 0.043 1841 Dihedral : 5.360 54.847 1523 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.12 % Allowed : 15.58 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.99 (0.23), residues: 1343 helix: 1.68 (0.23), residues: 523 sheet: 0.60 (0.31), residues: 283 loop : -0.27 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 169 HIS 0.004 0.001 HIS L 97 PHE 0.023 0.001 PHE B 95 TYR 0.030 0.001 TYR L 146 ARG 0.008 0.001 ARG H 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 4) link_NAG-ASN : angle 1.99941 ( 12) hydrogen bonds : bond 0.03730 ( 535) hydrogen bonds : angle 4.52560 ( 1482) SS BOND : bond 0.00404 ( 5) SS BOND : angle 3.17729 ( 10) covalent geometry : bond 0.00286 (10797) covalent geometry : angle 0.62822 (14714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 ASP cc_start: 0.7517 (t0) cc_final: 0.7243 (t0) REVERT: A 507 MET cc_start: 0.8091 (mtm) cc_final: 0.7676 (ttm) REVERT: A 528 ASP cc_start: 0.7424 (t0) cc_final: 0.7205 (t0) REVERT: B 145 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7951 (mp10) REVERT: B 294 LEU cc_start: 0.7562 (tp) cc_final: 0.7134 (tp) REVERT: B 369 GLN cc_start: 0.7087 (tp40) cc_final: 0.6372 (tm-30) REVERT: B 386 LEU cc_start: 0.8830 (mt) cc_final: 0.8571 (mt) REVERT: B 391 LYS cc_start: 0.7946 (mmpt) cc_final: 0.7123 (ptpp) REVERT: B 454 THR cc_start: 0.7144 (p) cc_final: 0.6799 (t) REVERT: B 483 LYS cc_start: 0.6635 (mmpt) cc_final: 0.6379 (mmmt) REVERT: L 189 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8005 (tptm) REVERT: H 166 LEU cc_start: 0.7811 (mt) cc_final: 0.7601 (mp) REVERT: H 216 LYS cc_start: 0.7937 (tptp) cc_final: 0.7618 (tptp) outliers start: 36 outliers final: 21 residues processed: 155 average time/residue: 0.2266 time to fit residues: 51.0557 Evaluate side-chains 144 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 431 CYS Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 189 LYS Chi-restraints excluded: chain L residue 211 ILE Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 124 optimal weight: 0.0040 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 117 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: B 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.162917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129125 restraints weight = 14888.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122242 restraints weight = 21304.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120328 restraints weight = 22848.229| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10806 Z= 0.112 Angle : 0.607 13.330 14736 Z= 0.300 Chirality : 0.042 0.192 1700 Planarity : 0.004 0.039 1841 Dihedral : 5.098 54.355 1523 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.29 % Allowed : 15.93 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.12 (0.23), residues: 1343 helix: 1.87 (0.23), residues: 521 sheet: 0.70 (0.31), residues: 284 loop : -0.31 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 169 HIS 0.003 0.001 HIS L 97 PHE 0.026 0.002 PHE B 402 TYR 0.030 0.001 TYR H 129 ARG 0.005 0.000 ARG L 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 4) link_NAG-ASN : angle 1.49159 ( 12) hydrogen bonds : bond 0.03471 ( 535) hydrogen bonds : angle 4.37522 ( 1482) SS BOND : bond 0.00292 ( 5) SS BOND : angle 1.60249 ( 10) covalent geometry : bond 0.00243 (10797) covalent geometry : angle 0.60478 (14714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.637 Fit side-chains revert: symmetry clash REVERT: A 475 ASP cc_start: 0.7572 (t0) cc_final: 0.7347 (t0) REVERT: A 507 MET cc_start: 0.8081 (mtm) cc_final: 0.7723 (ttm) REVERT: B 145 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7998 (mp10) REVERT: B 294 LEU cc_start: 0.7467 (tp) cc_final: 0.7045 (tp) REVERT: B 305 MET cc_start: 0.7585 (mtp) cc_final: 0.7375 (mtm) REVERT: B 314 ASP cc_start: 0.7910 (m-30) cc_final: 0.7525 (m-30) REVERT: B 369 GLN cc_start: 0.6548 (tp40) cc_final: 0.5936 (tm-30) REVERT: B 370 LEU cc_start: 0.7416 (mt) cc_final: 0.7113 (mt) REVERT: B 391 LYS cc_start: 0.7777 (mmpt) cc_final: 0.7170 (ptpp) REVERT: B 483 LYS cc_start: 0.6878 (mmpt) cc_final: 0.6666 (mmmt) REVERT: H 115 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8749 (tt) REVERT: H 129 TYR cc_start: 0.7980 (m-80) cc_final: 0.7513 (m-10) REVERT: H 166 LEU cc_start: 0.7721 (mt) cc_final: 0.7518 (mp) REVERT: H 216 LYS cc_start: 0.7844 (tptp) cc_final: 0.7546 (tptp) outliers start: 38 outliers final: 20 residues processed: 161 average time/residue: 0.3237 time to fit residues: 78.3672 Evaluate side-chains 145 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 431 CYS Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 211 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 105 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 0.0470 chunk 67 optimal weight: 9.9990 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.160340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.133100 restraints weight = 14987.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.132254 restraints weight = 26119.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.129413 restraints weight = 23695.085| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10806 Z= 0.196 Angle : 0.648 11.440 14736 Z= 0.318 Chirality : 0.044 0.291 1700 Planarity : 0.004 0.045 1841 Dihedral : 5.202 55.635 1523 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.94 % Allowed : 17.32 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.09 (0.23), residues: 1343 helix: 1.77 (0.23), residues: 521 sheet: 0.75 (0.31), residues: 288 loop : -0.29 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 169 HIS 0.009 0.001 HIS L 97 PHE 0.019 0.002 PHE A 541 TYR 0.030 0.002 TYR H 103 ARG 0.007 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 4) link_NAG-ASN : angle 1.50358 ( 12) hydrogen bonds : bond 0.03673 ( 535) hydrogen bonds : angle 4.46929 ( 1482) SS BOND : bond 0.00354 ( 5) SS BOND : angle 1.37530 ( 10) covalent geometry : bond 0.00466 (10797) covalent geometry : angle 0.64632 (14714) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 3.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 SER cc_start: 0.8494 (p) cc_final: 0.8210 (t) REVERT: A 475 ASP cc_start: 0.7785 (t0) cc_final: 0.7582 (t0) REVERT: A 507 MET cc_start: 0.8137 (mtm) cc_final: 0.7688 (ttm) REVERT: A 572 VAL cc_start: 0.9410 (t) cc_final: 0.9180 (m) REVERT: B 294 LEU cc_start: 0.7291 (tp) cc_final: 0.6908 (tp) REVERT: B 369 GLN cc_start: 0.6507 (tp40) cc_final: 0.5791 (tm-30) REVERT: B 391 LYS cc_start: 0.7759 (mmpt) cc_final: 0.7157 (ptpp) REVERT: L 181 MET cc_start: 0.8154 (tpt) cc_final: 0.7792 (tpt) REVERT: H 115 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8744 (tt) outliers start: 34 outliers final: 27 residues processed: 151 average time/residue: 0.4366 time to fit residues: 95.9796 Evaluate side-chains 143 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 431 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 211 ILE Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 111 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 107 optimal weight: 0.0980 chunk 3 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.161554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134655 restraints weight = 14769.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133957 restraints weight = 23095.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131786 restraints weight = 22028.622| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10806 Z= 0.139 Angle : 0.643 14.398 14736 Z= 0.311 Chirality : 0.043 0.294 1700 Planarity : 0.004 0.042 1841 Dihedral : 5.150 54.765 1523 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.03 % Allowed : 18.10 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.23), residues: 1343 helix: 1.75 (0.23), residues: 524 sheet: 0.80 (0.31), residues: 287 loop : -0.32 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP L 169 HIS 0.005 0.001 HIS L 97 PHE 0.021 0.002 PHE B 402 TYR 0.030 0.002 TYR L 146 ARG 0.006 0.000 ARG H 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 4) link_NAG-ASN : angle 1.38238 ( 12) hydrogen bonds : bond 0.03520 ( 535) hydrogen bonds : angle 4.40031 ( 1482) SS BOND : bond 0.00281 ( 5) SS BOND : angle 1.02620 ( 10) covalent geometry : bond 0.00318 (10797) covalent geometry : angle 0.64183 (14714) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 SER cc_start: 0.8326 (p) cc_final: 0.8047 (t) REVERT: A 475 ASP cc_start: 0.7808 (t0) cc_final: 0.7587 (t0) REVERT: A 507 MET cc_start: 0.8060 (mtm) cc_final: 0.7635 (ttm) REVERT: A 572 VAL cc_start: 0.9403 (t) cc_final: 0.9164 (m) REVERT: B 141 ARG cc_start: 0.7681 (mtp85) cc_final: 0.7164 (mtp85) REVERT: B 145 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7861 (mp10) REVERT: B 294 LEU cc_start: 0.7209 (tp) cc_final: 0.6860 (tp) REVERT: B 305 MET cc_start: 0.7324 (mtp) cc_final: 0.7013 (mtm) REVERT: B 314 ASP cc_start: 0.7775 (m-30) cc_final: 0.7563 (m-30) REVERT: B 359 LEU cc_start: 0.7471 (mt) cc_final: 0.7259 (mt) REVERT: B 369 GLN cc_start: 0.6236 (tp40) cc_final: 0.5867 (tm-30) REVERT: B 370 LEU cc_start: 0.6624 (mm) cc_final: 0.6240 (mt) REVERT: B 391 LYS cc_start: 0.7721 (mmpt) cc_final: 0.7154 (ptpp) REVERT: B 421 ARG cc_start: 0.6353 (tpp80) cc_final: 0.6146 (mmp80) REVERT: L 57 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8872 (p) REVERT: H 115 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8824 (tt) REVERT: H 217 ILE cc_start: 0.7651 (mm) cc_final: 0.7411 (mm) outliers start: 35 outliers final: 25 residues processed: 152 average time/residue: 0.3121 time to fit residues: 68.7189 Evaluate side-chains 146 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 431 CYS Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 1 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 chunk 100 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.161996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.136154 restraints weight = 15002.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.135545 restraints weight = 23588.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134111 restraints weight = 20726.289| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10806 Z= 0.123 Angle : 0.642 13.108 14736 Z= 0.309 Chirality : 0.043 0.284 1700 Planarity : 0.004 0.040 1841 Dihedral : 5.082 54.410 1523 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.25 % Allowed : 18.61 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.11 (0.23), residues: 1343 helix: 1.76 (0.23), residues: 524 sheet: 0.81 (0.31), residues: 289 loop : -0.29 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP L 169 HIS 0.004 0.001 HIS L 97 PHE 0.022 0.001 PHE B 402 TYR 0.029 0.001 TYR H 129 ARG 0.005 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 4) link_NAG-ASN : angle 1.35174 ( 12) hydrogen bonds : bond 0.03439 ( 535) hydrogen bonds : angle 4.35864 ( 1482) SS BOND : bond 0.00254 ( 5) SS BOND : angle 0.95378 ( 10) covalent geometry : bond 0.00277 (10797) covalent geometry : angle 0.64089 (14714) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 ASP cc_start: 0.7805 (t0) cc_final: 0.7563 (t0) REVERT: A 507 MET cc_start: 0.7993 (mtm) cc_final: 0.7569 (ttm) REVERT: A 572 VAL cc_start: 0.9353 (t) cc_final: 0.9081 (m) REVERT: A 609 LEU cc_start: 0.8685 (mt) cc_final: 0.8277 (mt) REVERT: B 141 ARG cc_start: 0.7323 (mtp85) cc_final: 0.6920 (mtp85) REVERT: B 145 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7869 (mp10) REVERT: B 294 LEU cc_start: 0.7154 (tp) cc_final: 0.6814 (tp) REVERT: B 305 MET cc_start: 0.7373 (mtp) cc_final: 0.7166 (mtm) REVERT: B 359 LEU cc_start: 0.7395 (mt) cc_final: 0.7179 (mt) REVERT: B 391 LYS cc_start: 0.7707 (mmpt) cc_final: 0.7175 (ptpp) REVERT: L 57 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8859 (p) REVERT: H 115 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8730 (tt) outliers start: 26 outliers final: 22 residues processed: 151 average time/residue: 0.2370 time to fit residues: 52.3581 Evaluate side-chains 143 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 431 CYS Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 27 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 78 optimal weight: 0.0010 chunk 103 optimal weight: 20.0000 chunk 37 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN B 420 HIS H 206 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.163209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.139494 restraints weight = 14769.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.133106 restraints weight = 20887.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131799 restraints weight = 24409.685| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 10806 Z= 0.110 Angle : 0.635 12.824 14736 Z= 0.305 Chirality : 0.043 0.278 1700 Planarity : 0.004 0.040 1841 Dihedral : 5.022 53.949 1523 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.25 % Allowed : 19.31 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.12 (0.23), residues: 1343 helix: 1.73 (0.23), residues: 527 sheet: 0.86 (0.31), residues: 289 loop : -0.28 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP L 169 HIS 0.007 0.001 HIS B 367 PHE 0.017 0.001 PHE B 445 TYR 0.044 0.001 TYR L 146 ARG 0.007 0.000 ARG B 421 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 4) link_NAG-ASN : angle 1.31668 ( 12) hydrogen bonds : bond 0.03291 ( 535) hydrogen bonds : angle 4.31340 ( 1482) SS BOND : bond 0.00235 ( 5) SS BOND : angle 0.76675 ( 10) covalent geometry : bond 0.00245 (10797) covalent geometry : angle 0.63391 (14714) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 475 ASP cc_start: 0.7754 (t0) cc_final: 0.7514 (t0) REVERT: A 507 MET cc_start: 0.7977 (mtm) cc_final: 0.7571 (ttm) REVERT: A 572 VAL cc_start: 0.9134 (t) cc_final: 0.8838 (m) REVERT: A 609 LEU cc_start: 0.8561 (mt) cc_final: 0.8091 (mt) REVERT: B 294 LEU cc_start: 0.7173 (tp) cc_final: 0.6805 (tp) REVERT: B 305 MET cc_start: 0.7414 (mtp) cc_final: 0.7038 (mtm) REVERT: B 359 LEU cc_start: 0.7412 (mt) cc_final: 0.7183 (mt) REVERT: B 391 LYS cc_start: 0.7732 (mmpt) cc_final: 0.7181 (ptpp) REVERT: B 421 ARG cc_start: 0.6262 (mmp80) cc_final: 0.5795 (ttm-80) REVERT: L 111 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7150 (mm-30) REVERT: H 115 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8728 (tt) outliers start: 26 outliers final: 18 residues processed: 145 average time/residue: 0.2296 time to fit residues: 47.9747 Evaluate side-chains 140 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 431 CYS Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 86 optimal weight: 8.9990 chunk 66 optimal weight: 0.0370 chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 72 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.163546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135823 restraints weight = 14756.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135077 restraints weight = 22118.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133148 restraints weight = 21911.815| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10806 Z= 0.114 Angle : 0.661 12.469 14736 Z= 0.318 Chirality : 0.042 0.259 1700 Planarity : 0.004 0.038 1841 Dihedral : 5.003 53.956 1523 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.99 % Allowed : 20.09 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.14 (0.23), residues: 1343 helix: 1.77 (0.23), residues: 525 sheet: 0.94 (0.32), residues: 287 loop : -0.32 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP L 169 HIS 0.004 0.001 HIS B 367 PHE 0.024 0.001 PHE B 402 TYR 0.026 0.001 TYR H 129 ARG 0.004 0.000 ARG L 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 4) link_NAG-ASN : angle 1.31308 ( 12) hydrogen bonds : bond 0.03202 ( 535) hydrogen bonds : angle 4.32374 ( 1482) SS BOND : bond 0.00248 ( 5) SS BOND : angle 0.73434 ( 10) covalent geometry : bond 0.00253 (10797) covalent geometry : angle 0.66047 (14714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4177.81 seconds wall clock time: 78 minutes 17.16 seconds (4697.16 seconds total)