Starting phenix.real_space_refine on Wed Feb 4 11:23:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wp8_37711/02_2026/8wp8_37711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wp8_37711/02_2026/8wp8_37711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wp8_37711/02_2026/8wp8_37711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wp8_37711/02_2026/8wp8_37711.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wp8_37711/02_2026/8wp8_37711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wp8_37711/02_2026/8wp8_37711.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4869 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 4185 2.51 5 N 1068 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6539 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "B" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1493 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 11, 'TRANS': 172} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" 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 Time building chain proxies: 2.37, per 1000 atoms: 0.36 Number of scatterers: 6539 At special positions: 0 Unit cell: (77.97, 87.63, 117.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 36 16.00 O 1249 8.00 N 1068 7.00 C 4185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG A 702 " - " ASN A 53 " " NAG A 703 " - " ASN A 322 " " NAG A 704 " - " ASN A 432 " " NAG B 601 " - " ASN B 354 " " NAG B 602 " - " ASN B 343 " " NAG C 1 " - " ASN A 90 " " NAG D 1 " - " ASN A 546 " " NAG E 1 " - " ASN A 103 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 390.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1474 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 5 sheets defined 55.0% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.147A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.565A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.776A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 158 through 173 removed outlier: 3.780A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.632A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.956A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.748A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.912A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.560A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.649A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.613A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.653A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.817A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.588A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.639A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.245A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.701A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.609A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.227A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 268 hydrogen bonds defined for protein. 759 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: 0.88 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1185 1.33 - 1.45: 1904 1.45 - 1.57: 3581 1.57 - 1.69: 0 1.69 - 1.82: 57 Bond restraints: 6727 Sorted by residual: bond pdb=" C PRO B 491 " pdb=" O PRO B 491 " ideal model delta sigma weight residual 1.239 1.205 0.034 1.27e-02 6.20e+03 7.14e+00 bond pdb=" N PHE B 490 " pdb=" CA PHE B 490 " ideal model delta sigma weight residual 1.452 1.490 -0.037 1.41e-02 5.03e+03 7.05e+00 bond pdb=" N LEU B 492 " pdb=" CA LEU B 492 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.23e-02 6.61e+03 5.97e+00 bond pdb=" N PRO B 491 " pdb=" CA PRO B 491 " ideal model delta sigma weight residual 1.469 1.445 0.024 1.25e-02 6.40e+03 3.73e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.08e+00 ... (remaining 6722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 8846 1.40 - 2.80: 229 2.80 - 4.20: 46 4.20 - 5.60: 16 5.60 - 7.00: 5 Bond angle restraints: 9142 Sorted by residual: angle pdb=" N PHE B 338 " pdb=" CA PHE B 338 " pdb=" C PHE B 338 " ideal model delta sigma weight residual 114.31 108.01 6.30 1.29e+00 6.01e-01 2.38e+01 angle pdb=" CA PHE B 490 " pdb=" C PHE B 490 " pdb=" N PRO B 491 " ideal model delta sigma weight residual 117.67 121.79 -4.12 1.01e+00 9.80e-01 1.66e+01 angle pdb=" N CYS B 361 " pdb=" CA CYS B 361 " pdb=" C CYS B 361 " ideal model delta sigma weight residual 107.88 112.87 -4.99 1.41e+00 5.03e-01 1.25e+01 angle pdb=" C GLU A 171 " pdb=" N VAL A 172 " pdb=" CA VAL A 172 " ideal model delta sigma weight residual 122.63 118.69 3.94 1.19e+00 7.06e-01 1.10e+01 angle pdb=" C LEU B 492 " pdb=" N GLN B 493 " pdb=" CA GLN B 493 " ideal model delta sigma weight residual 121.94 127.24 -5.30 1.76e+00 3.23e-01 9.06e+00 ... (remaining 9137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 3840 21.98 - 43.96: 235 43.96 - 65.94: 22 65.94 - 87.92: 23 87.92 - 109.90: 8 Dihedral angle restraints: 4128 sinusoidal: 1831 harmonic: 2297 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -9.72 -76.28 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 164.97 -71.97 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -119.82 33.82 1 1.00e+01 1.00e-02 1.62e+01 ... (remaining 4125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 964 0.106 - 0.212: 17 0.212 - 0.317: 3 0.317 - 0.423: 0 0.423 - 0.529: 2 Chirality restraints: 986 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 983 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 602 " 0.303 2.00e-02 2.50e+03 2.55e-01 8.12e+02 pdb=" C7 NAG B 602 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 602 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG B 602 " -0.437 2.00e-02 2.50e+03 pdb=" O7 NAG B 602 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 601 " 0.044 2.00e-02 2.50e+03 3.66e-02 1.67e+01 pdb=" C7 NAG B 601 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG B 601 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG B 601 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG B 601 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 354 " 0.014 2.00e-02 2.50e+03 1.69e-02 3.56e+00 pdb=" CG ASN B 354 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN B 354 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 354 " -0.028 2.00e-02 2.50e+03 pdb=" C1 NAG B 601 " 0.020 2.00e-02 2.50e+03 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 73 2.66 - 3.22: 5961 3.22 - 3.78: 9514 3.78 - 4.34: 12755 4.34 - 4.90: 21373 Nonbonded interactions: 49676 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.100 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.118 2.230 nonbonded pdb=" OG SER B 469 " pdb=" OE1 GLU B 471 " model vdw 2.246 3.040 nonbonded pdb=" O PHE A 327 " pdb=" OG SER A 331 " model vdw 2.283 3.040 nonbonded pdb=" O MET A 152 " pdb=" NH2 ARG A 161 " model vdw 2.315 3.120 ... (remaining 49671 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 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.480 Find NCS groups from input model: 0.040 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 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 : 0.005 0.209 6748 Z= 0.204 Angle : 0.635 12.236 9193 Z= 0.313 Chirality : 0.049 0.529 986 Planarity : 0.008 0.255 1164 Dihedral : 15.475 109.902 2636 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.24 (0.31), residues: 777 helix: 1.72 (0.29), residues: 362 sheet: -1.07 (0.89), residues: 32 loop : -1.32 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.013 0.001 TYR B 489 PHE 0.019 0.001 PHE B 515 TRP 0.023 0.001 TRP A 203 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6727) covalent geometry : angle 0.58428 ( 9142) SS BOND : bond 0.00152 ( 6) SS BOND : angle 0.62947 ( 12) hydrogen bonds : bond 0.16329 ( 268) hydrogen bonds : angle 6.00395 ( 759) metal coordination : bond 0.20307 ( 2) link_BETA1-4 : bond 0.00669 ( 5) link_BETA1-4 : angle 2.62598 ( 15) link_NAG-ASN : bond 0.00609 ( 8) link_NAG-ASN : angle 4.47105 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.7688 (tp) cc_final: 0.7455 (tt) REVERT: A 190 MET cc_start: 0.7344 (tmm) cc_final: 0.7134 (tmt) REVERT: A 218 SER cc_start: 0.8610 (t) cc_final: 0.8227 (p) REVERT: A 227 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6924 (mm-30) REVERT: A 368 ASP cc_start: 0.6784 (m-30) cc_final: 0.6568 (m-30) REVERT: A 471 ASP cc_start: 0.7591 (p0) cc_final: 0.7355 (p0) REVERT: A 536 GLU cc_start: 0.6453 (tm-30) cc_final: 0.6221 (tm-30) REVERT: A 544 ILE cc_start: 0.8361 (pt) cc_final: 0.8003 (mp) REVERT: A 547 SER cc_start: 0.7799 (t) cc_final: 0.7148 (p) REVERT: B 420 ASP cc_start: 0.7445 (m-30) cc_final: 0.7239 (m-30) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.5513 time to fit residues: 112.8010 Evaluate side-chains 169 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.0470 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 401 HIS A 535 HIS A 572 ASN B 339 HIS B 409 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.149443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.127467 restraints weight = 11578.343| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.67 r_work: 0.3517 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6748 Z= 0.150 Angle : 0.640 13.072 9193 Z= 0.312 Chirality : 0.049 0.540 986 Planarity : 0.004 0.040 1164 Dihedral : 8.832 67.445 1118 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.18 % Allowed : 11.64 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.24 (0.31), residues: 777 helix: 1.58 (0.29), residues: 365 sheet: -0.68 (0.87), residues: 32 loop : -1.23 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 460 TYR 0.016 0.001 TYR A 202 PHE 0.016 0.001 PHE B 515 TRP 0.010 0.001 TRP A 203 HIS 0.005 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6727) covalent geometry : angle 0.60229 ( 9142) SS BOND : bond 0.00392 ( 6) SS BOND : angle 0.75739 ( 12) hydrogen bonds : bond 0.05699 ( 268) hydrogen bonds : angle 4.79644 ( 759) metal coordination : bond 0.00542 ( 2) link_BETA1-4 : bond 0.00592 ( 5) link_BETA1-4 : angle 2.48532 ( 15) link_NAG-ASN : bond 0.00360 ( 8) link_NAG-ASN : angle 3.84526 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.7859 (tp) cc_final: 0.7570 (tt) REVERT: A 88 ILE cc_start: 0.8204 (pt) cc_final: 0.7674 (pp) REVERT: A 126 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8383 (tt) REVERT: A 149 ASN cc_start: 0.7899 (m-40) cc_final: 0.7618 (m-40) REVERT: A 192 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7844 (mtt-85) REVERT: A 227 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7508 (mm-30) REVERT: A 471 ASP cc_start: 0.7960 (p0) cc_final: 0.7678 (p0) REVERT: A 483 GLU cc_start: 0.7601 (tt0) cc_final: 0.7336 (tm-30) REVERT: A 489 GLU cc_start: 0.8077 (pm20) cc_final: 0.7746 (pm20) REVERT: A 536 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6845 (tm-30) REVERT: A 544 ILE cc_start: 0.8582 (pt) cc_final: 0.8369 (mp) REVERT: B 405 ASN cc_start: 0.8360 (p0) cc_final: 0.7879 (p0) REVERT: B 420 ASP cc_start: 0.7808 (m-30) cc_final: 0.7549 (m-30) outliers start: 15 outliers final: 6 residues processed: 180 average time/residue: 0.5100 time to fit residues: 96.7410 Evaluate side-chains 167 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 210 ASN A 572 ASN B 339 HIS B 439 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.148121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.125118 restraints weight = 13800.707| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.98 r_work: 0.3468 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6748 Z= 0.142 Angle : 0.617 12.314 9193 Z= 0.299 Chirality : 0.047 0.516 986 Planarity : 0.004 0.038 1164 Dihedral : 6.314 52.313 1118 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.20 % Allowed : 15.43 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.27 (0.31), residues: 777 helix: 1.63 (0.29), residues: 360 sheet: -0.94 (0.90), residues: 34 loop : -1.17 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.017 0.001 TYR B 489 PHE 0.016 0.001 PHE B 515 TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6727) covalent geometry : angle 0.58057 ( 9142) SS BOND : bond 0.00346 ( 6) SS BOND : angle 0.72051 ( 12) hydrogen bonds : bond 0.05662 ( 268) hydrogen bonds : angle 4.57788 ( 759) metal coordination : bond 0.00270 ( 2) link_BETA1-4 : bond 0.00646 ( 5) link_BETA1-4 : angle 2.35027 ( 15) link_NAG-ASN : bond 0.00514 ( 8) link_NAG-ASN : angle 3.67985 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7933 (mtt) REVERT: A 149 ASN cc_start: 0.7944 (m-40) cc_final: 0.7599 (m-40) REVERT: A 169 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7010 (mtt-85) REVERT: A 227 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7476 (mm-30) REVERT: A 249 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.6542 (ttm) REVERT: A 471 ASP cc_start: 0.8079 (p0) cc_final: 0.7787 (p0) REVERT: A 483 GLU cc_start: 0.7716 (tt0) cc_final: 0.7358 (tm-30) REVERT: A 527 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: A 536 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6921 (tm-30) REVERT: A 544 ILE cc_start: 0.8628 (pt) cc_final: 0.8371 (mp) REVERT: B 405 ASN cc_start: 0.8451 (p0) cc_final: 0.7974 (p0) REVERT: B 420 ASP cc_start: 0.7875 (m-30) cc_final: 0.7578 (m-30) outliers start: 22 outliers final: 7 residues processed: 167 average time/residue: 0.5344 time to fit residues: 94.0078 Evaluate side-chains 163 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 527 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN B 437 ASN B 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.146542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121464 restraints weight = 22523.777| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.86 r_work: 0.3380 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6748 Z= 0.159 Angle : 0.608 11.568 9193 Z= 0.297 Chirality : 0.046 0.511 986 Planarity : 0.004 0.044 1164 Dihedral : 5.260 52.214 1118 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.20 % Allowed : 15.14 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.29 (0.31), residues: 777 helix: 1.67 (0.28), residues: 354 sheet: -0.77 (0.91), residues: 34 loop : -1.17 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 559 TYR 0.017 0.002 TYR A 202 PHE 0.018 0.002 PHE A 308 TRP 0.011 0.001 TRP B 436 HIS 0.005 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 6727) covalent geometry : angle 0.57455 ( 9142) SS BOND : bond 0.00361 ( 6) SS BOND : angle 0.75938 ( 12) hydrogen bonds : bond 0.05921 ( 268) hydrogen bonds : angle 4.45146 ( 759) metal coordination : bond 0.00259 ( 2) link_BETA1-4 : bond 0.00550 ( 5) link_BETA1-4 : angle 2.16236 ( 15) link_NAG-ASN : bond 0.00451 ( 8) link_NAG-ASN : angle 3.55381 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8424 (ttp) cc_final: 0.8211 (ttm) REVERT: A 123 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7980 (mtt) REVERT: A 149 ASN cc_start: 0.8009 (m-40) cc_final: 0.7744 (m-40) REVERT: A 169 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7157 (mtt-85) REVERT: A 174 LYS cc_start: 0.8691 (mttm) cc_final: 0.8475 (mttp) REVERT: A 227 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7676 (mm-30) REVERT: A 249 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6811 (ttm) REVERT: A 471 ASP cc_start: 0.8139 (p0) cc_final: 0.7855 (p0) REVERT: A 483 GLU cc_start: 0.7831 (tt0) cc_final: 0.7496 (tm-30) REVERT: A 527 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7742 (tp30) REVERT: A 536 GLU cc_start: 0.7273 (tm-30) cc_final: 0.7070 (tm-30) REVERT: A 544 ILE cc_start: 0.8724 (pt) cc_final: 0.8464 (mp) REVERT: B 405 ASN cc_start: 0.8534 (p0) cc_final: 0.8050 (p0) REVERT: B 420 ASP cc_start: 0.8007 (m-30) cc_final: 0.7713 (m-30) REVERT: B 468 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8323 (mp) outliers start: 22 outliers final: 10 residues processed: 167 average time/residue: 0.5204 time to fit residues: 91.3544 Evaluate side-chains 162 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 44 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN B 437 ASN B 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.147111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123025 restraints weight = 18941.040| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.52 r_work: 0.3412 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6748 Z= 0.146 Angle : 0.607 11.494 9193 Z= 0.298 Chirality : 0.046 0.490 986 Planarity : 0.004 0.040 1164 Dihedral : 5.037 52.299 1118 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.35 % Allowed : 16.16 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.32 (0.31), residues: 777 helix: 1.68 (0.28), residues: 354 sheet: -1.28 (0.76), residues: 44 loop : -1.05 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 559 TYR 0.021 0.002 TYR B 423 PHE 0.017 0.001 PHE A 308 TRP 0.011 0.001 TRP B 436 HIS 0.014 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6727) covalent geometry : angle 0.57513 ( 9142) SS BOND : bond 0.00346 ( 6) SS BOND : angle 0.71881 ( 12) hydrogen bonds : bond 0.05708 ( 268) hydrogen bonds : angle 4.37130 ( 759) metal coordination : bond 0.00227 ( 2) link_BETA1-4 : bond 0.00498 ( 5) link_BETA1-4 : angle 1.96218 ( 15) link_NAG-ASN : bond 0.00498 ( 8) link_NAG-ASN : angle 3.52104 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7683 (tp30) cc_final: 0.7270 (tp30) REVERT: A 123 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7948 (mtt) REVERT: A 149 ASN cc_start: 0.7980 (m-40) cc_final: 0.7714 (m-40) REVERT: A 249 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6638 (ttm) REVERT: A 483 GLU cc_start: 0.7703 (tt0) cc_final: 0.7451 (tm-30) REVERT: A 527 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7649 (tp30) REVERT: A 536 GLU cc_start: 0.7211 (tm-30) cc_final: 0.7011 (tm-30) REVERT: B 405 ASN cc_start: 0.8530 (p0) cc_final: 0.8025 (p0) REVERT: B 420 ASP cc_start: 0.7930 (m-30) cc_final: 0.7625 (m-30) REVERT: B 437 ASN cc_start: 0.8664 (t0) cc_final: 0.8354 (t0) REVERT: B 468 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8297 (mp) outliers start: 23 outliers final: 10 residues processed: 153 average time/residue: 0.5378 time to fit residues: 86.6524 Evaluate side-chains 156 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 39 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.147308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.126432 restraints weight = 9473.072| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.38 r_work: 0.3520 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6748 Z= 0.137 Angle : 0.600 11.275 9193 Z= 0.297 Chirality : 0.045 0.472 986 Planarity : 0.004 0.039 1164 Dihedral : 4.929 52.329 1118 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.20 % Allowed : 17.18 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.35 (0.31), residues: 777 helix: 1.68 (0.29), residues: 360 sheet: -1.29 (0.75), residues: 44 loop : -1.05 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 192 TYR 0.020 0.001 TYR B 489 PHE 0.016 0.001 PHE A 308 TRP 0.011 0.001 TRP B 436 HIS 0.007 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6727) covalent geometry : angle 0.56985 ( 9142) SS BOND : bond 0.00316 ( 6) SS BOND : angle 0.67463 ( 12) hydrogen bonds : bond 0.05491 ( 268) hydrogen bonds : angle 4.27469 ( 759) metal coordination : bond 0.00181 ( 2) link_BETA1-4 : bond 0.00513 ( 5) link_BETA1-4 : angle 1.83008 ( 15) link_NAG-ASN : bond 0.00500 ( 8) link_NAG-ASN : angle 3.43007 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7656 (tp30) cc_final: 0.7227 (tp30) REVERT: A 123 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7932 (mtt) REVERT: A 149 ASN cc_start: 0.8027 (m-40) cc_final: 0.7703 (m-40) REVERT: A 249 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6967 (ttm) REVERT: A 252 TYR cc_start: 0.8182 (m-80) cc_final: 0.7968 (m-80) REVERT: A 376 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8218 (mtt) REVERT: A 483 GLU cc_start: 0.7808 (tt0) cc_final: 0.7448 (tm-30) REVERT: A 527 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7826 (tp30) REVERT: A 536 GLU cc_start: 0.7345 (tm-30) cc_final: 0.7114 (tm-30) REVERT: A 544 ILE cc_start: 0.8675 (pt) cc_final: 0.8448 (mt) REVERT: B 405 ASN cc_start: 0.8552 (p0) cc_final: 0.8094 (p0) REVERT: B 420 ASP cc_start: 0.7962 (m-30) cc_final: 0.7631 (m-30) REVERT: B 437 ASN cc_start: 0.8725 (t0) cc_final: 0.8411 (t0) outliers start: 22 outliers final: 10 residues processed: 158 average time/residue: 0.5144 time to fit residues: 85.7825 Evaluate side-chains 161 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 0.0980 chunk 44 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN B 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.147056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.125279 restraints weight = 11631.610| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.67 r_work: 0.3488 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6748 Z= 0.143 Angle : 0.614 11.118 9193 Z= 0.301 Chirality : 0.045 0.460 986 Planarity : 0.004 0.042 1164 Dihedral : 4.869 52.445 1118 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.93 % Allowed : 16.45 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.38 (0.32), residues: 777 helix: 1.70 (0.29), residues: 360 sheet: -1.19 (0.76), residues: 44 loop : -1.04 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 192 TYR 0.019 0.001 TYR B 423 PHE 0.016 0.001 PHE A 308 TRP 0.011 0.001 TRP B 436 HIS 0.005 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6727) covalent geometry : angle 0.58298 ( 9142) SS BOND : bond 0.00346 ( 6) SS BOND : angle 0.69120 ( 12) hydrogen bonds : bond 0.05540 ( 268) hydrogen bonds : angle 4.20755 ( 759) metal coordination : bond 0.00201 ( 2) link_BETA1-4 : bond 0.00530 ( 5) link_BETA1-4 : angle 1.77386 ( 15) link_NAG-ASN : bond 0.00496 ( 8) link_NAG-ASN : angle 3.54110 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7430 (tp30) cc_final: 0.6992 (tp30) REVERT: A 123 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7896 (mtt) REVERT: A 149 ASN cc_start: 0.7912 (m-40) cc_final: 0.7636 (m-40) REVERT: A 150 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7526 (tm-30) REVERT: A 167 SER cc_start: 0.8361 (t) cc_final: 0.8126 (p) REVERT: A 201 ASP cc_start: 0.7439 (t0) cc_final: 0.6999 (t0) REVERT: A 219 ARG cc_start: 0.8783 (mtm-85) cc_final: 0.8525 (mtp180) REVERT: A 249 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6483 (ttm) REVERT: A 483 GLU cc_start: 0.7549 (tt0) cc_final: 0.7275 (tm-30) REVERT: A 536 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6805 (tm-30) REVERT: B 405 ASN cc_start: 0.8507 (p0) cc_final: 0.8013 (p0) REVERT: B 420 ASP cc_start: 0.7765 (m-30) cc_final: 0.7457 (m-30) REVERT: B 437 ASN cc_start: 0.8622 (t0) cc_final: 0.8309 (t0) outliers start: 27 outliers final: 11 residues processed: 153 average time/residue: 0.5215 time to fit residues: 84.2131 Evaluate side-chains 152 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 0.0870 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN B 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.146915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.123019 restraints weight = 17297.521| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.39 r_work: 0.3431 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6748 Z= 0.142 Angle : 0.603 11.656 9193 Z= 0.297 Chirality : 0.045 0.446 986 Planarity : 0.004 0.040 1164 Dihedral : 4.819 52.478 1118 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.20 % Allowed : 18.20 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.39 (0.32), residues: 777 helix: 1.73 (0.28), residues: 360 sheet: -1.13 (0.75), residues: 44 loop : -1.06 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 192 TYR 0.020 0.001 TYR B 489 PHE 0.016 0.001 PHE A 308 TRP 0.011 0.001 TRP B 436 HIS 0.006 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 6727) covalent geometry : angle 0.57524 ( 9142) SS BOND : bond 0.00314 ( 6) SS BOND : angle 0.65228 ( 12) hydrogen bonds : bond 0.05544 ( 268) hydrogen bonds : angle 4.15053 ( 759) metal coordination : bond 0.00173 ( 2) link_BETA1-4 : bond 0.00502 ( 5) link_BETA1-4 : angle 1.70592 ( 15) link_NAG-ASN : bond 0.00463 ( 8) link_NAG-ASN : angle 3.36300 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7539 (tp30) cc_final: 0.7077 (tp30) REVERT: A 123 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7930 (mtt) REVERT: A 149 ASN cc_start: 0.7969 (m-40) cc_final: 0.7712 (m-40) REVERT: A 150 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 201 ASP cc_start: 0.7448 (t0) cc_final: 0.7189 (t0) REVERT: A 249 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6684 (ttm) REVERT: A 483 GLU cc_start: 0.7677 (tt0) cc_final: 0.7372 (tm-30) REVERT: A 536 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6917 (tm-30) REVERT: B 405 ASN cc_start: 0.8539 (p0) cc_final: 0.8069 (p0) REVERT: B 420 ASP cc_start: 0.7861 (m-30) cc_final: 0.7544 (m-30) REVERT: B 437 ASN cc_start: 0.8652 (t0) cc_final: 0.8364 (t0) outliers start: 22 outliers final: 14 residues processed: 151 average time/residue: 0.5251 time to fit residues: 83.5196 Evaluate side-chains 157 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.0170 chunk 53 optimal weight: 0.7980 chunk 7 optimal weight: 0.0870 chunk 16 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 chunk 68 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 228 HIS B 439 ASN B 493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.149051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.128097 restraints weight = 9510.025| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.40 r_work: 0.3545 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 6748 Z= 0.110 Angle : 0.586 11.943 9193 Z= 0.283 Chirality : 0.044 0.419 986 Planarity : 0.004 0.038 1164 Dihedral : 4.765 52.672 1118 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.33 % Allowed : 19.80 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.38 (0.32), residues: 777 helix: 1.62 (0.28), residues: 374 sheet: -1.22 (0.77), residues: 42 loop : -1.05 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 192 TYR 0.022 0.001 TYR B 489 PHE 0.013 0.001 PHE A 308 TRP 0.011 0.001 TRP B 436 HIS 0.007 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 6727) covalent geometry : angle 0.55648 ( 9142) SS BOND : bond 0.00277 ( 6) SS BOND : angle 0.51744 ( 12) hydrogen bonds : bond 0.04704 ( 268) hydrogen bonds : angle 4.02570 ( 759) metal coordination : bond 0.00043 ( 2) link_BETA1-4 : bond 0.00580 ( 5) link_BETA1-4 : angle 1.66245 ( 15) link_NAG-ASN : bond 0.00630 ( 8) link_NAG-ASN : angle 3.42822 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7670 (tp30) cc_final: 0.7235 (tp30) REVERT: A 123 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7910 (mtt) REVERT: A 149 ASN cc_start: 0.8034 (m-40) cc_final: 0.7801 (m-40) REVERT: A 150 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7694 (tm-30) REVERT: A 201 ASP cc_start: 0.7425 (t0) cc_final: 0.7143 (t0) REVERT: A 249 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6984 (ttm) REVERT: A 471 ASP cc_start: 0.8156 (p0) cc_final: 0.7885 (p0) REVERT: A 483 GLU cc_start: 0.7826 (tt0) cc_final: 0.7466 (tm-30) REVERT: A 536 GLU cc_start: 0.7298 (tm-30) cc_final: 0.7081 (tm-30) REVERT: B 405 ASN cc_start: 0.8553 (p0) cc_final: 0.8092 (p0) REVERT: B 420 ASP cc_start: 0.7908 (m-30) cc_final: 0.7635 (m-30) outliers start: 16 outliers final: 7 residues processed: 149 average time/residue: 0.5344 time to fit residues: 83.8691 Evaluate side-chains 147 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 0.0040 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 0.0980 chunk 47 optimal weight: 0.0370 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.0070 chunk 61 optimal weight: 7.9990 overall best weight: 0.1688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN B 437 ASN B 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.151436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127813 restraints weight = 17377.009| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.40 r_work: 0.3496 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 6748 Z= 0.102 Angle : 0.570 13.061 9193 Z= 0.274 Chirality : 0.043 0.412 986 Planarity : 0.004 0.038 1164 Dihedral : 4.662 52.794 1118 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.18 % Allowed : 20.09 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.42 (0.32), residues: 777 helix: 1.62 (0.28), residues: 380 sheet: -1.29 (0.77), residues: 42 loop : -1.01 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 192 TYR 0.020 0.001 TYR A 202 PHE 0.009 0.001 PHE B 515 TRP 0.011 0.001 TRP B 436 HIS 0.007 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 6727) covalent geometry : angle 0.54345 ( 9142) SS BOND : bond 0.00225 ( 6) SS BOND : angle 0.40273 ( 12) hydrogen bonds : bond 0.04117 ( 268) hydrogen bonds : angle 3.91314 ( 759) metal coordination : bond 0.00069 ( 2) link_BETA1-4 : bond 0.00523 ( 5) link_BETA1-4 : angle 1.60573 ( 15) link_NAG-ASN : bond 0.00707 ( 8) link_NAG-ASN : angle 3.22670 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7536 (tp30) cc_final: 0.7144 (tp30) REVERT: A 123 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7845 (mtt) REVERT: A 149 ASN cc_start: 0.7950 (m-40) cc_final: 0.7747 (m-40) REVERT: A 150 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7593 (tm-30) REVERT: A 249 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6748 (ttm) REVERT: A 349 TRP cc_start: 0.8604 (m100) cc_final: 0.8390 (m100) REVERT: A 471 ASP cc_start: 0.8054 (p0) cc_final: 0.7768 (p0) REVERT: A 483 GLU cc_start: 0.7664 (tt0) cc_final: 0.7364 (tm-30) REVERT: A 536 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6908 (tm-30) REVERT: B 405 ASN cc_start: 0.8511 (p0) cc_final: 0.8035 (p0) REVERT: B 420 ASP cc_start: 0.7741 (m-30) cc_final: 0.7490 (m-30) outliers start: 15 outliers final: 7 residues processed: 146 average time/residue: 0.5382 time to fit residues: 82.8804 Evaluate side-chains 140 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.9980 chunk 47 optimal weight: 0.0370 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN B 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127052 restraints weight = 18926.619| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.51 r_work: 0.3482 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 6748 Z= 0.142 Angle : 0.974 59.195 9193 Z= 0.552 Chirality : 0.044 0.408 986 Planarity : 0.004 0.065 1164 Dihedral : 4.680 52.791 1118 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.60 % Allowed : 21.40 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.40 (0.32), residues: 777 helix: 1.59 (0.28), residues: 380 sheet: -1.29 (0.77), residues: 42 loop : -1.01 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 192 TYR 0.021 0.001 TYR A 202 PHE 0.010 0.001 PHE B 515 TRP 0.010 0.001 TRP B 436 HIS 0.007 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6727) covalent geometry : angle 0.96047 ( 9142) SS BOND : bond 0.00250 ( 6) SS BOND : angle 0.37914 ( 12) hydrogen bonds : bond 0.04236 ( 268) hydrogen bonds : angle 3.94928 ( 759) metal coordination : bond 0.00207 ( 2) link_BETA1-4 : bond 0.00613 ( 5) link_BETA1-4 : angle 1.60490 ( 15) link_NAG-ASN : bond 0.00652 ( 8) link_NAG-ASN : angle 3.23838 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2897.63 seconds wall clock time: 50 minutes 5.47 seconds (3005.47 seconds total)