Starting phenix.real_space_refine on Thu Jul 2 07:01:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8l_36073/07_2026/8j8l_36073_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8l_36073/07_2026/8j8l_36073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j8l_36073/07_2026/8j8l_36073_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8l_36073/07_2026/8j8l_36073_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j8l_36073/07_2026/8j8l_36073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8l_36073/07_2026/8j8l_36073.map" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.039 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 27 5.16 5 C 4809 2.51 5 N 1187 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7361 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3656 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain: "B" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3579 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 24, 'TRANS': 438} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Time building chain proxies: 1.57, per 1000 atoms: 0.21 Number of scatterers: 7361 At special positions: 0 Unit cell: (99.645, 83.22, 129.21, 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 27 16.00 O 1338 8.00 N 1187 7.00 C 4809 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 260.4 milliseconds 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1718 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 58.7% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 179 through 207 Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.756A pdb=" N HIS A 221 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 222' Processing helix chain 'A' and resid 230 through 235 removed outlier: 4.445A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 287 through 302 Processing helix chain 'A' and resid 324 through 342 removed outlier: 3.575A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.728A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.624A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.615A pdb=" N THR A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 450 through 460 removed outlier: 3.628A pdb=" N PHE A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 585 through 589 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.660A pdb=" N VAL B 70 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 79 removed outlier: 3.946A pdb=" N LEU B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 110 removed outlier: 3.536A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 removed outlier: 4.000A pdb=" N GLU B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 158 removed outlier: 4.789A pdb=" N ARG B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Proline residue: B 142 - end of helix 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: 3.756A pdb=" N ALA B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 221 removed outlier: 3.678A pdb=" N ALA B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 269 through 298 removed outlier: 3.627A pdb=" N ASN B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Proline residue: B 275 - end of helix Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 310 through 321 removed outlier: 3.645A pdb=" N HIS B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 321 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 357 removed outlier: 4.647A pdb=" N ARG B 348 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 389 removed outlier: 4.003A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 422 removed outlier: 3.929A pdb=" N SER B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP B 417 " --> pdb=" O ILE B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 451 removed outlier: 4.270A pdb=" N PHE B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 439 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 447 " --> pdb=" O CYS B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 476 removed outlier: 3.865A pdb=" N ILE B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) Proline residue: B 470 - end of helix removed outlier: 3.895A pdb=" N GLY B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 227 removed outlier: 3.590A pdb=" N PHE A 467 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 262 removed outlier: 6.853A pdb=" N LEU A 307 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ARG A 349 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 400 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 267 Processing sheet with id=AA4, first strand: chain 'A' and resid 541 through 545 removed outlier: 3.568A pdb=" N PHE A 545 " --> pdb=" O SER A 553 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 621 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY A 622 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER A 599 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU A 624 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 597 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 626 " --> pdb=" O ASP A 595 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 575 through 576 removed outlier: 3.569A pdb=" N LEU A 575 " --> pdb=" O LEU A 617 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2166 1.34 - 1.46: 1276 1.46 - 1.58: 4060 1.58 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 7542 Sorted by residual: bond pdb=" C4 NAG F 1 " pdb=" O4 NAG F 1 " ideal model delta sigma weight residual 1.409 1.477 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" CE2 DAH B 601 " pdb=" OE2 DAH B 601 " ideal model delta sigma weight residual 1.351 1.401 -0.050 2.00e-02 2.50e+03 6.20e+00 bond pdb=" CZ DAH B 601 " pdb=" OZ DAH B 601 " ideal model delta sigma weight residual 1.356 1.400 -0.044 2.00e-02 2.50e+03 4.88e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.64e+00 bond pdb=" C3 NAG F 1 " pdb=" O3 NAG F 1 " ideal model delta sigma weight residual 1.403 1.435 -0.032 2.00e-02 2.50e+03 2.49e+00 ... (remaining 7537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 10060 2.15 - 4.29: 176 4.29 - 6.44: 29 6.44 - 8.58: 5 8.58 - 10.73: 1 Bond angle restraints: 10271 Sorted by residual: angle pdb=" C LEU B 138 " pdb=" N ILE B 139 " pdb=" CA ILE B 139 " ideal model delta sigma weight residual 123.16 119.05 4.11 1.06e+00 8.90e-01 1.50e+01 angle pdb=" CA DAH B 601 " pdb=" CB DAH B 601 " pdb=" CG DAH B 601 " ideal model delta sigma weight residual 112.94 102.21 10.73 3.00e+00 1.11e-01 1.28e+01 angle pdb=" N ILE B 429 " pdb=" CA ILE B 429 " pdb=" C ILE B 429 " ideal model delta sigma weight residual 113.22 117.46 -4.24 1.23e+00 6.61e-01 1.19e+01 angle pdb=" N PRO B 428 " pdb=" CA PRO B 428 " pdb=" C PRO B 428 " ideal model delta sigma weight residual 112.47 119.32 -6.85 2.06e+00 2.36e-01 1.11e+01 angle pdb=" N GLU B 78 " pdb=" CA GLU B 78 " pdb=" C GLU B 78 " ideal model delta sigma weight residual 114.31 110.14 4.17 1.29e+00 6.01e-01 1.05e+01 ... (remaining 10266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.38: 4232 25.38 - 50.76: 236 50.76 - 76.14: 31 76.14 - 101.53: 15 101.53 - 126.91: 11 Dihedral angle restraints: 4525 sinusoidal: 1852 harmonic: 2673 Sorted by residual: dihedral pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " pdb=" C5 NAG D 2 " ideal model delta sinusoidal sigma weight residual -62.96 63.95 -126.91 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" C2 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sinusoidal sigma weight residual 175.11 56.03 119.08 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" O3 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sinusoidal sigma weight residual 295.45 176.99 118.46 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 4522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.279: 1209 0.279 - 0.558: 1 0.558 - 0.837: 1 0.837 - 1.117: 0 1.117 - 1.396: 1 Chirality restraints: 1212 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.22e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.43e+01 ... (remaining 1209 not shown) Planarity restraints: 1275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.328 2.00e-02 2.50e+03 2.82e-01 9.96e+02 pdb=" C7 NAG D 2 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.026 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.490 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.300 2.00e-02 2.50e+03 2.52e-01 7.94e+02 pdb=" C7 NAG D 1 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.431 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.294 2.00e-02 2.50e+03 2.50e-01 7.79e+02 pdb=" C7 NAG F 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.182 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.430 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.030 2.00e-02 2.50e+03 ... (remaining 1272 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 873 2.75 - 3.28: 7800 3.28 - 3.82: 12211 3.82 - 4.36: 13372 4.36 - 4.90: 22899 Nonbonded interactions: 57155 Sorted by model distance: nonbonded pdb=" OD2 ASP A 356 " pdb=" OG SER A 359 " model vdw 2.207 3.040 nonbonded pdb=" NH2 ARG B 419 " pdb=" O LYS B 422 " model vdw 2.217 3.120 nonbonded pdb=" OD1 ASN A 366 " pdb=" C8 NAG D 2 " model vdw 2.219 3.460 nonbonded pdb=" O TYR A 251 " pdb=" OG SER A 254 " model vdw 2.247 3.040 nonbonded pdb=" O ILE B 268 " pdb=" ND2 ASN B 273 " model vdw 2.256 3.120 ... (remaining 57150 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.120 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.250 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 7551 Z= 0.219 Angle : 0.819 26.608 10297 Z= 0.383 Chirality : 0.062 1.396 1212 Planarity : 0.016 0.282 1271 Dihedral : 17.586 126.907 2804 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.89 % Allowed : 0.89 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.29), residues: 928 helix: 1.32 (0.25), residues: 481 sheet: 0.09 (0.67), residues: 59 loop : -1.48 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 614 TYR 0.015 0.001 TYR B 289 PHE 0.014 0.001 PHE B 402 TRP 0.006 0.001 TRP A 184 HIS 0.004 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 ( 7542) covalent geometry : angle 0.68872 / 0.35 (10271) SS BOND : bond 0.00274 / 0.14 ( 1) SS BOND : angle 1.28614 / 0.72 ( 2) hydrogen bonds : bond 0.18774 / 12.43 ( 379) hydrogen bonds : angle 6.82108 / 4.90 ( 1095) link_BETA1-4 : bond 0.01903 / 0.95 ( 4) link_BETA1-4 : angle 4.89330 / 2.87 ( 12) link_NAG-ASN : bond 0.10309 / 5.27 ( 4) link_NAG-ASN : angle 12.07163 / 9.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 ASP cc_start: 0.8006 (m-30) cc_final: 0.7689 (m-30) REVERT: B 84 LEU cc_start: 0.9120 (tp) cc_final: 0.8914 (tt) REVERT: B 141 ARG cc_start: 0.8992 (mmp80) cc_final: 0.8547 (mmp80) REVERT: B 259 TYR cc_start: 0.8902 (m-80) cc_final: 0.8506 (m-80) REVERT: B 383 MET cc_start: 0.8573 (tpp) cc_final: 0.7994 (mpp) outliers start: 7 outliers final: 2 residues processed: 107 average time/residue: 0.0662 time to fit residues: 10.2156 Evaluate side-chains 66 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 431 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.0020 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.062864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.045886 restraints weight = 38883.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.047353 restraints weight = 20750.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.048325 restraints weight = 14490.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.048875 restraints weight = 11692.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.049197 restraints weight = 10328.804| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7551 Z= 0.146 Angle : 0.746 11.083 10297 Z= 0.341 Chirality : 0.044 0.307 1212 Planarity : 0.005 0.048 1271 Dihedral : 14.509 103.410 1166 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.89 % Allowed : 10.42 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.28), residues: 928 helix: 1.74 (0.24), residues: 492 sheet: -0.30 (0.63), residues: 66 loop : -1.20 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 614 TYR 0.014 0.002 TYR B 103 PHE 0.025 0.001 PHE A 190 TRP 0.008 0.001 TRP B 325 HIS 0.006 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 ( 7542) covalent geometry : angle 0.71889 / 0.33 (10271) SS BOND : bond 0.00159 / 0.08 ( 1) SS BOND : angle 0.63283 / 0.37 ( 2) hydrogen bonds : bond 0.06205 / 4.30 ( 379) hydrogen bonds : angle 4.94616 / 3.52 ( 1095) link_BETA1-4 : bond 0.01158 / 0.55 ( 4) link_BETA1-4 : angle 3.79341 / 2.21 ( 12) link_NAG-ASN : bond 0.00495 / 0.25 ( 4) link_NAG-ASN : angle 4.51732 / 2.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9357 (pp) REVERT: A 471 ASP cc_start: 0.8088 (m-30) cc_final: 0.7683 (m-30) REVERT: A 508 MET cc_start: 0.9280 (ptp) cc_final: 0.8831 (ptp) REVERT: B 47 GLN cc_start: 0.8270 (mm110) cc_final: 0.8049 (mm-40) REVERT: B 141 ARG cc_start: 0.9192 (mmp80) cc_final: 0.8861 (mmp80) REVERT: B 262 PHE cc_start: 0.9490 (m-10) cc_final: 0.9284 (m-80) REVERT: B 267 MET cc_start: 0.9272 (mpp) cc_final: 0.8939 (pmm) REVERT: B 365 MET cc_start: 0.8114 (mmm) cc_final: 0.7830 (mmm) REVERT: B 383 MET cc_start: 0.9213 (tpp) cc_final: 0.8620 (mpp) outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.0624 time to fit residues: 7.4464 Evaluate side-chains 67 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 431 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.061481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.044273 restraints weight = 39900.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.045685 restraints weight = 21523.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.046583 restraints weight = 15213.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.047165 restraints weight = 12429.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.047490 restraints weight = 10985.002| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7551 Z= 0.170 Angle : 0.680 12.374 10297 Z= 0.316 Chirality : 0.042 0.208 1212 Planarity : 0.005 0.054 1271 Dihedral : 13.426 112.424 1164 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.02 % Allowed : 12.58 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.29), residues: 928 helix: 1.96 (0.24), residues: 488 sheet: -0.38 (0.65), residues: 66 loop : -1.11 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 614 TYR 0.014 0.002 TYR B 103 PHE 0.021 0.001 PHE B 402 TRP 0.012 0.001 TRP B 477 HIS 0.003 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 7542) covalent geometry : angle 0.66097 / 0.31 (10271) SS BOND : bond 0.00061 / 0.03 ( 1) SS BOND : angle 0.80284 / 0.46 ( 2) hydrogen bonds : bond 0.05342 / 3.73 ( 379) hydrogen bonds : angle 4.59965 / 3.26 ( 1095) link_BETA1-4 : bond 0.00989 / 0.49 ( 4) link_BETA1-4 : angle 3.13154 / 1.81 ( 12) link_NAG-ASN : bond 0.00365 / 0.18 ( 4) link_NAG-ASN : angle 3.64084 / 2.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9351 (pp) REVERT: A 471 ASP cc_start: 0.8107 (m-30) cc_final: 0.7698 (m-30) REVERT: A 508 MET cc_start: 0.9280 (ptp) cc_final: 0.8948 (ptp) REVERT: B 141 ARG cc_start: 0.9291 (mmp80) cc_final: 0.9090 (mmp80) REVERT: B 262 PHE cc_start: 0.9534 (m-10) cc_final: 0.9285 (m-80) REVERT: B 267 MET cc_start: 0.9303 (mpp) cc_final: 0.8919 (pmm) REVERT: B 365 MET cc_start: 0.8369 (mmm) cc_final: 0.7903 (mmm) REVERT: B 383 MET cc_start: 0.9239 (tpp) cc_final: 0.8669 (mpp) outliers start: 8 outliers final: 5 residues processed: 71 average time/residue: 0.0610 time to fit residues: 6.5302 Evaluate side-chains 63 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 431 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.5980 chunk 77 optimal weight: 0.0170 chunk 87 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 64 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 overall best weight: 2.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.043598 restraints weight = 40222.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.045036 restraints weight = 21612.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.045941 restraints weight = 15204.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.046501 restraints weight = 12366.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.046721 restraints weight = 10921.104| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7551 Z= 0.174 Angle : 0.669 9.714 10297 Z= 0.314 Chirality : 0.042 0.269 1212 Planarity : 0.004 0.049 1271 Dihedral : 12.251 111.138 1164 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.27 % Allowed : 14.74 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.29), residues: 928 helix: 1.98 (0.24), residues: 488 sheet: -0.54 (0.64), residues: 66 loop : -1.06 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 614 TYR 0.016 0.001 TYR B 472 PHE 0.014 0.001 PHE B 402 TRP 0.007 0.001 TRP B 477 HIS 0.003 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 7542) covalent geometry : angle 0.65037 / 0.31 (10271) SS BOND : bond 0.00065 / 0.03 ( 1) SS BOND : angle 0.75638 / 0.44 ( 2) hydrogen bonds : bond 0.04916 / 3.40 ( 379) hydrogen bonds : angle 4.38330 / 3.11 ( 1095) link_BETA1-4 : bond 0.00903 / 0.45 ( 4) link_BETA1-4 : angle 3.41343 / 1.98 ( 12) link_NAG-ASN : bond 0.00363 / 0.18 ( 4) link_NAG-ASN : angle 3.19728 / 1.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9358 (pp) REVERT: A 471 ASP cc_start: 0.8148 (m-30) cc_final: 0.7719 (m-30) REVERT: A 508 MET cc_start: 0.9234 (ptp) cc_final: 0.8919 (ptp) REVERT: B 138 LEU cc_start: 0.9081 (mt) cc_final: 0.8872 (mp) REVERT: B 262 PHE cc_start: 0.9531 (m-80) cc_final: 0.9278 (m-80) REVERT: B 267 MET cc_start: 0.9245 (mpp) cc_final: 0.8924 (pmm) REVERT: B 365 MET cc_start: 0.8470 (mmm) cc_final: 0.7175 (mmp) REVERT: B 383 MET cc_start: 0.9245 (tpp) cc_final: 0.8646 (mpp) outliers start: 10 outliers final: 8 residues processed: 67 average time/residue: 0.0617 time to fit residues: 6.3556 Evaluate side-chains 62 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 431 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.062352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.045609 restraints weight = 40130.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.047056 restraints weight = 22149.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.047972 restraints weight = 15839.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.048535 restraints weight = 12983.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.048852 restraints weight = 11530.161| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7551 Z= 0.115 Angle : 0.654 13.446 10297 Z= 0.295 Chirality : 0.040 0.232 1212 Planarity : 0.004 0.069 1271 Dihedral : 11.779 111.542 1164 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.78 % Allowed : 15.63 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.29), residues: 928 helix: 2.15 (0.24), residues: 485 sheet: -0.53 (0.64), residues: 66 loop : -1.01 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 614 TYR 0.009 0.001 TYR A 251 PHE 0.021 0.001 PHE B 402 TRP 0.006 0.001 TRP B 134 HIS 0.003 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 7542) covalent geometry : angle 0.63540 / 0.29 (10271) SS BOND : bond 0.00158 / 0.08 ( 1) SS BOND : angle 0.49698 / 0.29 ( 2) hydrogen bonds : bond 0.04409 / 3.08 ( 379) hydrogen bonds : angle 4.13335 / 2.93 ( 1095) link_BETA1-4 : bond 0.01025 / 0.51 ( 4) link_BETA1-4 : angle 3.38696 / 1.96 ( 12) link_NAG-ASN : bond 0.00504 / 0.25 ( 4) link_NAG-ASN : angle 3.14020 / 1.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9317 (pp) REVERT: A 471 ASP cc_start: 0.8105 (m-30) cc_final: 0.7668 (m-30) REVERT: A 508 MET cc_start: 0.9274 (ptp) cc_final: 0.8964 (ptp) REVERT: B 47 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7644 (mm-40) REVERT: B 267 MET cc_start: 0.9297 (mpp) cc_final: 0.8945 (pmm) REVERT: B 365 MET cc_start: 0.8507 (mmm) cc_final: 0.7135 (mmp) REVERT: B 383 MET cc_start: 0.9191 (tpp) cc_final: 0.8587 (mpp) outliers start: 14 outliers final: 7 residues processed: 78 average time/residue: 0.0718 time to fit residues: 7.9058 Evaluate side-chains 68 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 381 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 72 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.061445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.044690 restraints weight = 40241.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.046087 restraints weight = 22346.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.046969 restraints weight = 16047.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.047431 restraints weight = 13219.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.047829 restraints weight = 11896.288| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7551 Z= 0.156 Angle : 0.672 10.553 10297 Z= 0.309 Chirality : 0.041 0.235 1212 Planarity : 0.005 0.073 1271 Dihedral : 11.466 111.094 1163 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.78 % Allowed : 17.03 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.29), residues: 928 helix: 2.18 (0.24), residues: 488 sheet: -0.65 (0.63), residues: 66 loop : -0.99 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 355 TYR 0.011 0.001 TYR B 119 PHE 0.024 0.001 PHE B 402 TRP 0.011 0.001 TRP B 134 HIS 0.007 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 7542) covalent geometry : angle 0.65463 / 0.31 (10271) SS BOND : bond 0.00084 / 0.04 ( 1) SS BOND : angle 0.56914 / 0.33 ( 2) hydrogen bonds : bond 0.04414 / 3.08 ( 379) hydrogen bonds : angle 4.18896 / 2.97 ( 1095) link_BETA1-4 : bond 0.00904 / 0.45 ( 4) link_BETA1-4 : angle 3.33170 / 1.93 ( 12) link_NAG-ASN : bond 0.00316 / 0.16 ( 4) link_NAG-ASN : angle 3.05967 / 1.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9366 (pp) REVERT: A 471 ASP cc_start: 0.8104 (m-30) cc_final: 0.7675 (m-30) REVERT: A 508 MET cc_start: 0.9268 (ptp) cc_final: 0.8962 (ptp) REVERT: B 267 MET cc_start: 0.9217 (mpp) cc_final: 0.8813 (pmm) REVERT: B 365 MET cc_start: 0.8634 (mmm) cc_final: 0.7006 (tpp) outliers start: 14 outliers final: 9 residues processed: 70 average time/residue: 0.0704 time to fit residues: 7.2008 Evaluate side-chains 70 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 381 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 47 optimal weight: 0.0770 chunk 58 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.062470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.045814 restraints weight = 40386.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.047236 restraints weight = 22174.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.048144 restraints weight = 15822.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.048677 restraints weight = 12976.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.049028 restraints weight = 11583.560| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7551 Z= 0.118 Angle : 0.668 14.752 10297 Z= 0.300 Chirality : 0.041 0.247 1212 Planarity : 0.004 0.073 1271 Dihedral : 11.021 110.701 1163 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.52 % Allowed : 17.92 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.29), residues: 928 helix: 2.26 (0.24), residues: 485 sheet: -0.59 (0.63), residues: 66 loop : -0.95 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 614 TYR 0.009 0.001 TYR B 119 PHE 0.025 0.001 PHE B 402 TRP 0.010 0.001 TRP B 134 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 7542) covalent geometry : angle 0.65069 / 0.30 (10271) SS BOND : bond 0.00171 / 0.09 ( 1) SS BOND : angle 0.52007 / 0.31 ( 2) hydrogen bonds : bond 0.04093 / 2.85 ( 379) hydrogen bonds : angle 4.01084 / 2.84 ( 1095) link_BETA1-4 : bond 0.00983 / 0.49 ( 4) link_BETA1-4 : angle 3.43137 / 1.99 ( 12) link_NAG-ASN : bond 0.00401 / 0.20 ( 4) link_NAG-ASN : angle 3.01521 / 1.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9350 (pp) REVERT: A 471 ASP cc_start: 0.8137 (m-30) cc_final: 0.7718 (m-30) REVERT: A 508 MET cc_start: 0.9280 (ptp) cc_final: 0.8978 (ptp) REVERT: B 145 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.8837 (mp10) REVERT: B 262 PHE cc_start: 0.9381 (m-80) cc_final: 0.9108 (m-80) REVERT: B 267 MET cc_start: 0.9211 (mpp) cc_final: 0.8734 (pmm) REVERT: B 297 PHE cc_start: 0.8427 (t80) cc_final: 0.8038 (t80) REVERT: B 365 MET cc_start: 0.8599 (mmm) cc_final: 0.6940 (tpp) REVERT: B 383 MET cc_start: 0.9172 (tpp) cc_final: 0.8599 (mpp) outliers start: 12 outliers final: 6 residues processed: 76 average time/residue: 0.0697 time to fit residues: 7.4524 Evaluate side-chains 69 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 381 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 0.0270 chunk 11 optimal weight: 9.9990 chunk 68 optimal weight: 0.0000 chunk 50 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 overall best weight: 0.7846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.062787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.046020 restraints weight = 40201.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.047445 restraints weight = 22163.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048346 restraints weight = 15861.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.048871 restraints weight = 13043.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.049230 restraints weight = 11651.747| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7551 Z= 0.111 Angle : 0.692 13.368 10297 Z= 0.306 Chirality : 0.041 0.254 1212 Planarity : 0.004 0.074 1271 Dihedral : 10.622 109.962 1163 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.52 % Allowed : 18.17 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.29), residues: 928 helix: 2.26 (0.24), residues: 488 sheet: -0.49 (0.64), residues: 66 loop : -0.88 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 614 TYR 0.008 0.001 TYR B 248 PHE 0.025 0.001 PHE B 402 TRP 0.010 0.001 TRP B 134 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 7542) covalent geometry : angle 0.67541 / 0.30 (10271) SS BOND : bond 0.00142 / 0.07 ( 1) SS BOND : angle 0.49759 / 0.29 ( 2) hydrogen bonds : bond 0.03898 / 2.73 ( 379) hydrogen bonds : angle 3.99622 / 2.79 ( 1095) link_BETA1-4 : bond 0.00979 / 0.49 ( 4) link_BETA1-4 : angle 3.43571 / 1.99 ( 12) link_NAG-ASN : bond 0.00386 / 0.19 ( 4) link_NAG-ASN : angle 2.97212 / 1.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9324 (pp) REVERT: A 471 ASP cc_start: 0.8113 (m-30) cc_final: 0.7719 (m-30) REVERT: A 508 MET cc_start: 0.9269 (ptp) cc_final: 0.8970 (ptp) REVERT: B 262 PHE cc_start: 0.9353 (m-80) cc_final: 0.9101 (m-80) REVERT: B 365 MET cc_start: 0.8571 (mmm) cc_final: 0.6954 (tpp) outliers start: 12 outliers final: 7 residues processed: 77 average time/residue: 0.0701 time to fit residues: 7.8164 Evaluate side-chains 69 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 381 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 85 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.062424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.045656 restraints weight = 40089.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.047076 restraints weight = 22119.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.047977 restraints weight = 15812.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.048538 restraints weight = 13005.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.048828 restraints weight = 11556.154| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7551 Z= 0.123 Angle : 0.683 12.421 10297 Z= 0.308 Chirality : 0.042 0.258 1212 Planarity : 0.004 0.062 1271 Dihedral : 10.312 109.710 1163 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.65 % Allowed : 18.68 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.29), residues: 928 helix: 2.15 (0.24), residues: 494 sheet: -0.51 (0.64), residues: 66 loop : -0.82 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 614 TYR 0.009 0.001 TYR B 119 PHE 0.024 0.001 PHE B 402 TRP 0.012 0.001 TRP B 405 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 7542) covalent geometry : angle 0.66680 / 0.30 (10271) SS BOND : bond 0.00128 / 0.07 ( 1) SS BOND : angle 0.52700 / 0.31 ( 2) hydrogen bonds : bond 0.03905 / 2.74 ( 379) hydrogen bonds : angle 4.05006 / 2.85 ( 1095) link_BETA1-4 : bond 0.00964 / 0.48 ( 4) link_BETA1-4 : angle 3.42827 / 1.99 ( 12) link_NAG-ASN : bond 0.00307 / 0.15 ( 4) link_NAG-ASN : angle 2.89227 / 1.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9337 (pp) REVERT: A 471 ASP cc_start: 0.8110 (m-30) cc_final: 0.7703 (m-30) REVERT: A 508 MET cc_start: 0.9265 (ptp) cc_final: 0.8947 (ptp) REVERT: B 145 GLN cc_start: 0.9371 (OUTLIER) cc_final: 0.8788 (mp10) REVERT: B 262 PHE cc_start: 0.9351 (m-80) cc_final: 0.9121 (m-80) REVERT: B 365 MET cc_start: 0.8670 (mmm) cc_final: 0.7054 (tpp) outliers start: 13 outliers final: 9 residues processed: 74 average time/residue: 0.0730 time to fit residues: 7.6847 Evaluate side-chains 73 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 473 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.062093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.045322 restraints weight = 40104.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.046701 restraints weight = 22221.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.047588 restraints weight = 15924.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048135 restraints weight = 13111.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.048388 restraints weight = 11663.894| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7551 Z= 0.137 Angle : 0.701 12.100 10297 Z= 0.316 Chirality : 0.043 0.260 1212 Planarity : 0.004 0.053 1271 Dihedral : 9.995 109.735 1163 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.65 % Allowed : 18.93 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.29), residues: 928 helix: 2.18 (0.24), residues: 494 sheet: -0.52 (0.64), residues: 66 loop : -0.79 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 614 TYR 0.011 0.001 TYR B 119 PHE 0.025 0.001 PHE B 402 TRP 0.011 0.001 TRP B 134 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 7542) covalent geometry : angle 0.68493 / 0.31 (10271) SS BOND : bond 0.00117 / 0.06 ( 1) SS BOND : angle 0.55524 / 0.32 ( 2) hydrogen bonds : bond 0.03985 / 2.80 ( 379) hydrogen bonds : angle 4.10204 / 2.87 ( 1095) link_BETA1-4 : bond 0.00928 / 0.46 ( 4) link_BETA1-4 : angle 3.40529 / 1.98 ( 12) link_NAG-ASN : bond 0.00265 / 0.13 ( 4) link_NAG-ASN : angle 2.83179 / 1.62 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9338 (pp) REVERT: A 471 ASP cc_start: 0.8110 (m-30) cc_final: 0.7707 (m-30) REVERT: B 262 PHE cc_start: 0.9341 (m-80) cc_final: 0.9098 (m-80) REVERT: B 365 MET cc_start: 0.8673 (mmm) cc_final: 0.7052 (tpp) REVERT: B 383 MET cc_start: 0.9159 (tpp) cc_final: 0.8459 (mpp) outliers start: 13 outliers final: 11 residues processed: 71 average time/residue: 0.0632 time to fit residues: 6.5996 Evaluate side-chains 74 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 473 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.062805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.046050 restraints weight = 39751.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.047459 restraints weight = 21975.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.048367 restraints weight = 15735.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.048849 restraints weight = 12928.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.049214 restraints weight = 11604.458| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7551 Z= 0.115 Angle : 0.688 12.427 10297 Z= 0.308 Chirality : 0.042 0.262 1212 Planarity : 0.004 0.047 1271 Dihedral : 9.596 109.742 1163 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.52 % Allowed : 19.19 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.29), residues: 928 helix: 2.22 (0.24), residues: 492 sheet: -0.42 (0.64), residues: 66 loop : -0.84 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 614 TYR 0.011 0.001 TYR B 248 PHE 0.024 0.001 PHE B 402 TRP 0.011 0.001 TRP B 134 HIS 0.002 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 7542) covalent geometry : angle 0.67145 / 0.30 (10271) SS BOND : bond 0.00192 / 0.10 ( 1) SS BOND : angle 0.54669 / 0.32 ( 2) hydrogen bonds : bond 0.03760 / 2.63 ( 379) hydrogen bonds : angle 3.96865 / 2.78 ( 1095) link_BETA1-4 : bond 0.00982 / 0.49 ( 4) link_BETA1-4 : angle 3.50293 / 2.04 ( 12) link_NAG-ASN : bond 0.00359 / 0.18 ( 4) link_NAG-ASN : angle 2.72238 / 1.54 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1219.95 seconds wall clock time: 21 minutes 46.37 seconds (1306.37 seconds total)