Starting phenix.real_space_refine on Fri Sep 11 16:57:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5a63_3061/09_2026/5a63_3061.cif Found real_map, /net/cci-nas-00/data/ceres_data/5a63_3061/09_2026/5a63_3061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5a63_3061/09_2026/5a63_3061.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5a63_3061/09_2026/5a63_3061.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5a63_3061/09_2026/5a63_3061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5a63_3061/09_2026/5a63_3061.map" model { file = "/net/cci-nas-00/data/ceres_data/5a63_3061/09_2026/5a63_3061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5a63_3061/09_2026/5a63_3061.cif" } resolution = 3.4 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= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 35 5.16 5 C 6536 2.51 5 N 1589 2.21 5 O 1841 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10003 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5222 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 37, 'TRANS': 627} Chain: "B" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1702 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 6, 'TRANS': 208} Chain breaks: 2 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 850 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} 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 chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "G" 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 chiralities: 2 Chain: "H" 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 chiralities: 2 Chain: "I" 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 chiralities: 2 Chain: "J" 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 chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 1.97, per 1000 atoms: 0.20 Number of scatterers: 10003 At special positions: 0 Unit cell: (91, 147, 95.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 2 15.00 O 1841 8.00 N 1589 7.00 C 6536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.54 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=1.86 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=1.12 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 BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " BMA F 3 " - " BMA F 5 " NAG-ASN " NAG A1705 " - " ASN A 387 " " NAG A1712 " - " ASN A 464 " " NAG A1713 " - " ASN A 506 " " NAG A1714 " - " ASN A 264 " " NAG A1715 " - " ASN A 187 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 270.8 milliseconds 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2298 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 6 sheets defined 60.9% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 34 through 40 removed outlier: 3.949A pdb=" N ARG A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.515A pdb=" N LEU A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.558A pdb=" N MET A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.787A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.621A pdb=" N CYS A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 removed outlier: 4.047A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.665A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 434 removed outlier: 4.147A pdb=" N ALA A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 474 through 479 removed outlier: 4.239A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 503 Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.610A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 Processing helix chain 'A' and resid 541 through 546 removed outlier: 3.810A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.756A pdb=" N TYR A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 567 " --> pdb=" O THR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 665 through 693 Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'B' and resid 78 through 104 Proline residue: B 88 - end of helix removed outlier: 3.671A pdb=" N SER B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 108 Processing helix chain 'B' and resid 167 through 190 removed outlier: 4.219A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 241 Processing helix chain 'B' and resid 242 through 260 removed outlier: 3.544A pdb=" N ALA B 251 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 399 Processing helix chain 'B' and resid 404 through 428 Processing helix chain 'B' and resid 435 through 452 Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.288A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 24 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 28 through 61 Processing helix chain 'C' and resid 64 through 103 removed outlier: 3.851A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 142 removed outlier: 3.553A pdb=" N TYR C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 141 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.500A pdb=" N THR C 172 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 206 removed outlier: 3.786A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 232 removed outlier: 4.074A pdb=" N LEU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.651A pdb=" N LEU C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 removed outlier: 3.761A pdb=" N ARG D 5 " --> pdb=" O ASN D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 22 Processing helix chain 'D' and resid 26 through 36 Processing helix chain 'D' and resid 37 through 44 Processing helix chain 'D' and resid 49 through 85 removed outlier: 3.597A pdb=" N TRP D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) Proline residue: D 83 - end of helix Processing helix chain 'D' and resid 86 through 92 removed outlier: 3.813A pdb=" N ASP D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 41 through 44 removed outlier: 4.633A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 13.686A pdb=" N VAL A 75 " --> pdb=" O PRO A 211 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AC, first strand: chain 'A' and resid 175 through 176 Processing sheet with id=AD, first strand: chain 'A' and resid 412 through 414 removed outlier: 7.400A pdb=" N VAL A 277 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE A 362 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA A 279 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A 364 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG A 281 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N GLY A 366 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A 253 " --> pdb=" O ALA A 630 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.091A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.858A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1698 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: 1.16 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1535 1.31 - 1.44: 2969 1.44 - 1.56: 5683 1.56 - 1.69: 15 1.69 - 1.81: 53 Bond restraints: 10255 Sorted by residual: bond pdb=" C21 PC1 C1245 " pdb=" O21 PC1 C1245 " ideal model delta sigma weight residual 1.331 1.462 -0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" C LEU A 422 " pdb=" N PRO A 423 " ideal model delta sigma weight residual 1.329 1.406 -0.077 1.18e-02 7.18e+03 4.20e+01 bond pdb=" C31 PC1 C1245 " pdb=" O31 PC1 C1245 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.13e+01 bond pdb=" C21 PC1 B1468 " pdb=" O21 PC1 B1468 " ideal model delta sigma weight residual 1.331 1.459 -0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C31 PC1 B1468 " pdb=" O31 PC1 B1468 " ideal model delta sigma weight residual 1.330 1.455 -0.125 2.00e-02 2.50e+03 3.93e+01 ... (remaining 10250 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 13428 3.45 - 6.90: 483 6.90 - 10.35: 35 10.35 - 13.80: 9 13.80 - 17.25: 11 Bond angle restraints: 13966 Sorted by residual: angle pdb=" N THR A 372 " pdb=" CA THR A 372 " pdb=" C THR A 372 " ideal model delta sigma weight residual 111.14 122.90 -11.76 1.08e+00 8.57e-01 1.18e+02 angle pdb=" N LEU A 370 " pdb=" CA LEU A 370 " pdb=" C LEU A 370 " ideal model delta sigma weight residual 111.14 122.32 -11.18 1.08e+00 8.57e-01 1.07e+02 angle pdb=" N GLU A 161 " pdb=" CA GLU A 161 " pdb=" C GLU A 161 " ideal model delta sigma weight residual 111.14 122.01 -10.87 1.08e+00 8.57e-01 1.01e+02 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 119.78 -9.08 1.22e+00 6.72e-01 5.54e+01 angle pdb=" N GLU A 644 " pdb=" CA GLU A 644 " pdb=" C GLU A 644 " ideal model delta sigma weight residual 112.88 122.45 -9.57 1.29e+00 6.01e-01 5.50e+01 ... (remaining 13961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 4968 18.01 - 36.01: 559 36.01 - 54.02: 229 54.02 - 72.02: 58 72.02 - 90.03: 18 Dihedral angle restraints: 5832 sinusoidal: 2268 harmonic: 3564 Sorted by residual: dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -176.03 90.03 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CA PHE A 210 " pdb=" C PHE A 210 " pdb=" N PRO A 211 " pdb=" CA PRO A 211 " ideal model delta harmonic sigma weight residual 180.00 142.45 37.55 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -148.02 62.02 1 1.00e+01 1.00e-02 5.10e+01 ... (remaining 5829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.261: 1610 0.261 - 0.522: 43 0.522 - 0.783: 1 0.783 - 1.044: 0 1.044 - 1.305: 3 Chirality restraints: 1657 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.20e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 435 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.26e+01 chirality pdb=" C1 NAG A1712 " pdb=" ND2 ASN A 464 " pdb=" C2 NAG A1712 " pdb=" O5 NAG A1712 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-01 2.50e+01 4.05e+01 ... (remaining 1654 not shown) Planarity restraints: 1716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 187 " 0.193 2.00e-02 2.50e+03 1.93e-01 4.68e+02 pdb=" CG ASN A 187 " -0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN A 187 " -0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN A 187 " -0.295 2.00e-02 2.50e+03 pdb=" C1 NAG A1715 " 0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 387 " -0.132 2.00e-02 2.50e+03 1.30e-01 2.11e+02 pdb=" CG ASN A 387 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 387 " 0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN A 387 " 0.189 2.00e-02 2.50e+03 pdb=" C1 NAG A1705 " -0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 435 " -0.116 2.00e-02 2.50e+03 1.15e-01 1.65e+02 pdb=" CG ASN A 435 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 435 " 0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN A 435 " 0.177 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.134 2.00e-02 2.50e+03 ... (remaining 1713 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 232 2.64 - 3.21: 9953 3.21 - 3.77: 16667 3.77 - 4.34: 21756 4.34 - 4.90: 35642 Nonbonded interactions: 84250 Sorted by model distance: nonbonded pdb=" O GLY A 504 " pdb=" OG1 THR A 505 " model vdw 2.079 3.040 nonbonded pdb=" OD1 ASN A 324 " pdb=" N VAL A 325 " model vdw 2.123 3.120 nonbonded pdb=" OE1 GLU A 186 " pdb=" OG1 THR A 189 " model vdw 2.209 3.040 nonbonded pdb=" O TYR A 645 " pdb=" OG SER A 646 " model vdw 2.228 3.040 nonbonded pdb=" O HIS A 222 " pdb=" OG SER A 651 " model vdw 2.234 3.040 ... (remaining 84245 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 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 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: 0.360 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.640 Find NCS groups from input model: 0.070 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3972 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 : 0.015 0.915 10280 Z= 0.895 Angle : 1.816 28.019 14036 Z= 1.203 Chirality : 0.109 1.305 1657 Planarity : 0.008 0.106 1705 Dihedral : 19.070 86.887 3519 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 39.51 Ramachandran Plot: Outliers : 2.15 % Allowed : 6.36 % Favored : 91.49 % Rotamer: Outliers : 13.74 % Allowed : 12.12 % Favored : 74.14 % Cbeta Deviations : 0.70 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.17 % 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: -0.17 (0.22), residues: 1211 helix: 1.34 (0.17), residues: 672 sheet: -1.51 (0.48), residues: 113 loop : -2.13 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 657 TYR 0.031 0.003 TYR B 225 PHE 0.033 0.003 PHE B 386 TRP 0.021 0.002 TRP A 289 HIS 0.007 0.002 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00991 / 0.69 (10255) covalent geometry : angle 1.68869 / 1.18 (13966) SS BOND : bond 0.47461 / 32.42 ( 5) SS BOND : angle 13.39284 / 10.92 ( 10) hydrogen bonds : bond 0.16835 / 11.73 ( 580) hydrogen bonds : angle 6.76479 / 4.84 ( 1698) link_BETA1-3 : bond 0.00373 / 0.20 ( 1) link_BETA1-3 : angle 3.09807 / 1.69 ( 3) link_BETA1-4 : bond 0.00498 / 0.28 ( 7) link_BETA1-4 : angle 8.10627 / 5.49 ( 21) link_BETA1-6 : bond 0.00688 / 0.36 ( 1) link_BETA1-6 : angle 2.93101 / 1.58 ( 3) link_NAG-ASN : bond 0.14525 / 8.26 ( 11) link_NAG-ASN : angle 9.91942 / 6.81 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 299 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6219 (mtt180) cc_final: 0.5888 (mtm110) REVERT: A 80 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6251 (tt0) REVERT: A 167 LEU cc_start: 0.6419 (tp) cc_final: 0.6003 (tt) REVERT: A 204 ASN cc_start: 0.7695 (m-40) cc_final: 0.6810 (t0) REVERT: A 210 PHE cc_start: 0.5690 (t80) cc_final: 0.5373 (t80) REVERT: A 213 CYS cc_start: 0.7691 (t) cc_final: 0.7338 (t) REVERT: A 221 MET cc_start: 0.5818 (mmt) cc_final: 0.5582 (mmt) REVERT: A 380 THR cc_start: 0.7074 (OUTLIER) cc_final: 0.6744 (m) REVERT: A 418 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6884 (tt0) REVERT: A 464 ASN cc_start: 0.6011 (OUTLIER) cc_final: 0.5791 (t0) REVERT: A 516 GLN cc_start: 0.6494 (tt0) cc_final: 0.6256 (tp40) REVERT: A 541 ASP cc_start: 0.7815 (m-30) cc_final: 0.7436 (t0) REVERT: A 554 TYR cc_start: 0.6512 (t80) cc_final: 0.6214 (t80) REVERT: A 587 GLN cc_start: 0.7646 (tp-100) cc_final: 0.7051 (pt0) REVERT: A 654 LYS cc_start: 0.7917 (pttp) cc_final: 0.7677 (ttmt) REVERT: A 655 ASP cc_start: 0.6726 (m-30) cc_final: 0.6481 (p0) REVERT: B 167 ILE cc_start: 0.3599 (pp) cc_final: 0.3229 (tt) REVERT: B 194 ASP cc_start: 0.6497 (p0) cc_final: 0.6267 (p0) REVERT: C 109 ARG cc_start: 0.7007 (tpm-80) cc_final: 0.5863 (ttp-110) REVERT: D 6 VAL cc_start: 0.5954 (t) cc_final: 0.5754 (t) REVERT: D 44 VAL cc_start: 0.2103 (OUTLIER) cc_final: 0.1573 (t) outliers start: 144 outliers final: 53 residues processed: 395 average time/residue: 0.0922 time to fit residues: 50.9423 Evaluate side-chains 265 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 208 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 429 ARG Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 94 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 ASN A 150 ASN A 163 GLN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN A 305 GLN A 313 GLN A 367 GLN A 418 GLN A 428 GLN A 449 HIS ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN A 587 GLN A 606 GLN B 464 GLN C 136 ASN C 207 ASN D 79 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106702 restraints weight = 15417.605| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.34 r_work: 0.3108 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10280 Z= 0.201 Angle : 0.836 11.280 14036 Z= 0.416 Chirality : 0.052 0.378 1657 Planarity : 0.006 0.050 1705 Dihedral : 12.804 71.046 1494 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.87 % Favored : 94.72 % Rotamer: Outliers : 9.26 % Allowed : 17.75 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.09 % 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: 0.78 (0.25), residues: 1211 helix: 2.38 (0.20), residues: 687 sheet: -1.61 (0.43), residues: 120 loop : -2.26 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 622 TYR 0.021 0.002 TYR B 225 PHE 0.039 0.003 PHE B 465 TRP 0.028 0.002 TRP A 257 HIS 0.011 0.002 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (10255) covalent geometry : angle 0.81860 / 0.41 (13966) SS BOND : bond 0.02528 / 1.76 ( 5) SS BOND : angle 1.65289 / 1.01 ( 10) hydrogen bonds : bond 0.04682 / 3.17 ( 580) hydrogen bonds : angle 5.01680 / 3.55 ( 1698) link_BETA1-3 : bond 0.00226 / 0.12 ( 1) link_BETA1-3 : angle 1.64518 / 1.36 ( 3) link_BETA1-4 : bond 0.00560 / 0.33 ( 7) link_BETA1-4 : angle 2.79296 / 1.56 ( 21) link_BETA1-6 : bond 0.00177 / 0.09 ( 1) link_BETA1-6 : angle 1.21373 / 0.97 ( 3) link_NAG-ASN : bond 0.00574 / 0.31 ( 11) link_NAG-ASN : angle 2.77057 / 1.94 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 247 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8794 (mtt180) cc_final: 0.8351 (mtm110) REVERT: A 41 TYR cc_start: 0.9313 (m-80) cc_final: 0.8767 (m-80) REVERT: A 65 SER cc_start: 0.9077 (t) cc_final: 0.8722 (p) REVERT: A 69 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8655 (t0) REVERT: A 95 MET cc_start: 0.7815 (mtp) cc_final: 0.7295 (ttm) REVERT: A 104 THR cc_start: 0.9044 (m) cc_final: 0.8771 (p) REVERT: A 111 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8561 (tt) REVERT: A 156 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: A 167 LEU cc_start: 0.9293 (tp) cc_final: 0.8982 (tt) REVERT: A 186 GLU cc_start: 0.8028 (tp30) cc_final: 0.7794 (tp30) REVERT: A 204 ASN cc_start: 0.8032 (m-40) cc_final: 0.7034 (t0) REVERT: A 210 PHE cc_start: 0.8520 (t80) cc_final: 0.8289 (t80) REVERT: A 248 CYS cc_start: 0.6897 (OUTLIER) cc_final: 0.6593 (m) REVERT: A 347 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8015 (mtm) REVERT: A 428 GLN cc_start: 0.8378 (mt0) cc_final: 0.7980 (mt0) REVERT: A 431 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8616 (mp) REVERT: A 464 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8133 (t0) REVERT: A 472 SER cc_start: 0.5859 (OUTLIER) cc_final: 0.5637 (m) REVERT: A 507 PHE cc_start: 0.8415 (m-10) cc_final: 0.8173 (m-10) REVERT: A 587 GLN cc_start: 0.7694 (tp40) cc_final: 0.7226 (pt0) REVERT: A 646 SER cc_start: 0.9082 (p) cc_final: 0.8667 (t) REVERT: A 688 TYR cc_start: 0.8212 (t80) cc_final: 0.7935 (t80) REVERT: A 693 LYS cc_start: 0.8664 (mmtp) cc_final: 0.8293 (mtpp) REVERT: B 81 HIS cc_start: 0.8253 (t-90) cc_final: 0.7820 (m90) REVERT: B 233 MET cc_start: 0.8506 (tpt) cc_final: 0.8149 (tpt) REVERT: B 421 THR cc_start: 0.8931 (m) cc_final: 0.8617 (p) REVERT: B 429 LYS cc_start: 0.5858 (OUTLIER) cc_final: 0.4835 (mmtt) REVERT: B 437 ILE cc_start: 0.8352 (tt) cc_final: 0.7820 (mt) REVERT: B 446 TYR cc_start: 0.8332 (t80) cc_final: 0.8125 (t80) REVERT: C 96 LYS cc_start: 0.7334 (mttt) cc_final: 0.7085 (tptt) REVERT: C 109 ARG cc_start: 0.7603 (tpm-80) cc_final: 0.7162 (mtm110) REVERT: C 117 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8020 (ttm) REVERT: C 123 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8605 (tp) REVERT: C 180 ASP cc_start: 0.8309 (t70) cc_final: 0.8054 (t70) REVERT: C 184 ARG cc_start: 0.8414 (mmm-85) cc_final: 0.8075 (mtt180) REVERT: C 218 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7885 (m-80) outliers start: 97 outliers final: 42 residues processed: 307 average time/residue: 0.0921 time to fit residues: 41.0794 Evaluate side-chains 262 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 208 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 429 ARG Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 TRP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 114 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 58 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN C 207 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.100552 restraints weight = 15749.697| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.42 r_work: 0.3001 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10280 Z= 0.258 Angle : 0.802 9.628 14036 Z= 0.390 Chirality : 0.049 0.359 1657 Planarity : 0.005 0.049 1705 Dihedral : 10.936 66.896 1429 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.62 % Favored : 93.97 % Rotamer: Outliers : 8.21 % Allowed : 20.90 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.46 (0.25), residues: 1211 helix: 2.03 (0.19), residues: 680 sheet: -1.61 (0.44), residues: 123 loop : -2.16 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 84 TYR 0.023 0.002 TYR B 225 PHE 0.043 0.002 PHE B 465 TRP 0.016 0.002 TRP C 209 HIS 0.007 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.26 (10255) covalent geometry : angle 0.78557 / 0.39 (13966) SS BOND : bond 0.00914 / 0.47 ( 5) SS BOND : angle 1.92805 / 1.20 ( 10) hydrogen bonds : bond 0.04581 / 3.11 ( 580) hydrogen bonds : angle 4.89437 / 3.44 ( 1698) link_BETA1-3 : bond 0.00353 / 0.19 ( 1) link_BETA1-3 : angle 1.49657 / 1.25 ( 3) link_BETA1-4 : bond 0.00237 / 0.13 ( 7) link_BETA1-4 : angle 2.33281 / 1.34 ( 21) link_BETA1-6 : bond 0.00781 / 0.41 ( 1) link_BETA1-6 : angle 1.32179 / 1.06 ( 3) link_NAG-ASN : bond 0.00637 / 0.39 ( 11) link_NAG-ASN : angle 2.77182 / 1.91 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 219 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8871 (mtt180) cc_final: 0.8471 (mtm110) REVERT: A 65 SER cc_start: 0.8872 (t) cc_final: 0.8472 (p) REVERT: A 82 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8800 (mp) REVERT: A 95 MET cc_start: 0.8045 (mtp) cc_final: 0.7529 (ttm) REVERT: A 104 THR cc_start: 0.9022 (m) cc_final: 0.8631 (p) REVERT: A 156 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: A 167 LEU cc_start: 0.9301 (tp) cc_final: 0.8942 (tt) REVERT: A 186 GLU cc_start: 0.8068 (tp30) cc_final: 0.7760 (tp30) REVERT: A 347 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7981 (mmm) REVERT: A 355 GLN cc_start: 0.8335 (tp40) cc_final: 0.7691 (mm-40) REVERT: A 364 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: A 431 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8594 (mp) REVERT: A 587 GLN cc_start: 0.7859 (tp40) cc_final: 0.7243 (pt0) REVERT: A 688 TYR cc_start: 0.8289 (t80) cc_final: 0.8045 (t80) REVERT: A 693 LYS cc_start: 0.8627 (mmtp) cc_final: 0.8267 (mtpp) REVERT: A 695 ASP cc_start: 0.7557 (m-30) cc_final: 0.6612 (t70) REVERT: B 81 HIS cc_start: 0.8227 (t-90) cc_final: 0.7849 (m90) REVERT: B 228 MET cc_start: 0.7894 (mtp) cc_final: 0.7678 (mtp) REVERT: B 233 MET cc_start: 0.8789 (tpt) cc_final: 0.8541 (tpt) REVERT: B 245 THR cc_start: 0.7497 (m) cc_final: 0.7100 (p) REVERT: B 429 LYS cc_start: 0.5954 (OUTLIER) cc_final: 0.4746 (mmtt) REVERT: B 432 LEU cc_start: 0.4846 (OUTLIER) cc_final: 0.4265 (tt) REVERT: B 437 ILE cc_start: 0.7713 (tt) cc_final: 0.7203 (mt) REVERT: B 446 TYR cc_start: 0.8432 (t80) cc_final: 0.8156 (t80) REVERT: B 459 GLN cc_start: 0.8412 (mt0) cc_final: 0.8207 (mt0) REVERT: C 96 LYS cc_start: 0.7291 (mttt) cc_final: 0.6977 (tptt) REVERT: C 117 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8253 (mtm) REVERT: C 123 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8678 (tp) REVERT: C 180 ASP cc_start: 0.8368 (t70) cc_final: 0.8104 (t70) REVERT: C 184 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.8161 (mtm-85) REVERT: C 218 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7955 (m-80) outliers start: 86 outliers final: 51 residues processed: 275 average time/residue: 0.0902 time to fit residues: 36.0007 Evaluate side-chains 261 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 200 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 429 ARG Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 67 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 HIS A 102 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS D 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106385 restraints weight = 15687.738| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.49 r_work: 0.3082 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10280 Z= 0.155 Angle : 0.715 10.698 14036 Z= 0.347 Chirality : 0.046 0.351 1657 Planarity : 0.004 0.042 1705 Dihedral : 9.906 65.090 1414 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.79 % Favored : 94.80 % Rotamer: Outliers : 6.20 % Allowed : 22.61 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.41 (0.24), residues: 1211 helix: 1.91 (0.19), residues: 682 sheet: -1.61 (0.44), residues: 120 loop : -2.06 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 84 TYR 0.016 0.002 TYR B 225 PHE 0.043 0.002 PHE B 465 TRP 0.014 0.001 TRP A 257 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (10255) covalent geometry : angle 0.70248 / 0.34 (13966) SS BOND : bond 0.01425 / 0.72 ( 5) SS BOND : angle 0.85890 / 0.59 ( 10) hydrogen bonds : bond 0.04054 / 2.74 ( 580) hydrogen bonds : angle 4.68453 / 3.29 ( 1698) link_BETA1-3 : bond 0.00500 / 0.26 ( 1) link_BETA1-3 : angle 1.51838 / 1.22 ( 3) link_BETA1-4 : bond 0.00397 / 0.20 ( 7) link_BETA1-4 : angle 2.11753 / 1.19 ( 21) link_BETA1-6 : bond 0.00921 / 0.48 ( 1) link_BETA1-6 : angle 1.24313 / 1.02 ( 3) link_NAG-ASN : bond 0.00642 / 0.37 ( 11) link_NAG-ASN : angle 2.27548 / 1.59 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 235 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 SER cc_start: 0.8781 (t) cc_final: 0.8463 (p) REVERT: A 95 MET cc_start: 0.7945 (mtp) cc_final: 0.7455 (ttm) REVERT: A 104 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8660 (p) REVERT: A 167 LEU cc_start: 0.9232 (tp) cc_final: 0.8879 (tt) REVERT: A 305 GLN cc_start: 0.8923 (tp40) cc_final: 0.8638 (tp40) REVERT: A 347 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7820 (mmm) REVERT: A 355 GLN cc_start: 0.8345 (tp40) cc_final: 0.7720 (mm-40) REVERT: A 357 GLU cc_start: 0.8277 (tt0) cc_final: 0.8065 (tt0) REVERT: A 364 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: A 507 PHE cc_start: 0.8191 (m-80) cc_final: 0.7891 (m-80) REVERT: A 587 GLN cc_start: 0.8182 (tp40) cc_final: 0.7730 (pt0) REVERT: A 677 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.7020 (t80) REVERT: A 688 TYR cc_start: 0.8327 (t80) cc_final: 0.8099 (t80) REVERT: A 693 LYS cc_start: 0.8749 (mmtp) cc_final: 0.8394 (mtpp) REVERT: A 695 ASP cc_start: 0.7475 (m-30) cc_final: 0.6621 (t70) REVERT: B 93 MET cc_start: 0.7912 (mtp) cc_final: 0.7668 (mtm) REVERT: B 187 LYS cc_start: 0.8639 (mmtm) cc_final: 0.8420 (mmtm) REVERT: B 228 MET cc_start: 0.7880 (mtp) cc_final: 0.7632 (mtp) REVERT: B 233 MET cc_start: 0.8809 (tpt) cc_final: 0.8525 (tpt) REVERT: B 244 TRP cc_start: 0.7067 (OUTLIER) cc_final: 0.5872 (m-90) REVERT: B 245 THR cc_start: 0.7695 (m) cc_final: 0.7116 (p) REVERT: B 387 ILE cc_start: 0.9130 (mt) cc_final: 0.8896 (mp) REVERT: B 419 CYS cc_start: 0.8000 (m) cc_final: 0.7376 (t) REVERT: B 421 THR cc_start: 0.9104 (m) cc_final: 0.8762 (p) REVERT: B 429 LYS cc_start: 0.5973 (OUTLIER) cc_final: 0.4628 (mmtt) REVERT: B 432 LEU cc_start: 0.4903 (OUTLIER) cc_final: 0.4324 (tt) REVERT: B 446 TYR cc_start: 0.8475 (t80) cc_final: 0.8271 (t80) REVERT: B 450 ASP cc_start: 0.8049 (t0) cc_final: 0.7652 (t0) REVERT: B 459 GLN cc_start: 0.8274 (mt0) cc_final: 0.8045 (mt0) REVERT: C 96 LYS cc_start: 0.7281 (mttt) cc_final: 0.6960 (tptt) REVERT: C 109 ARG cc_start: 0.7590 (ttp-170) cc_final: 0.7249 (mtm110) REVERT: C 117 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8264 (mtm) REVERT: C 119 TYR cc_start: 0.8572 (t80) cc_final: 0.8313 (t80) REVERT: C 123 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8645 (tp) REVERT: C 180 ASP cc_start: 0.8345 (t70) cc_final: 0.8087 (t70) REVERT: C 210 TYR cc_start: 0.8800 (m-80) cc_final: 0.8597 (m-80) REVERT: D 9 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7182 (mp0) outliers start: 65 outliers final: 31 residues processed: 277 average time/residue: 0.0841 time to fit residues: 34.2747 Evaluate side-chains 258 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 218 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 654 LYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 TRP Chi-restraints excluded: chain D residue 94 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN A 516 GLN C 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.099567 restraints weight = 15905.539| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.44 r_work: 0.3020 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 10280 Z= 0.265 Angle : 0.773 10.268 14036 Z= 0.376 Chirality : 0.048 0.450 1657 Planarity : 0.005 0.046 1705 Dihedral : 9.219 61.440 1403 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.62 % Favored : 94.05 % Rotamer: Outliers : 7.63 % Allowed : 22.04 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.08 (0.24), residues: 1211 helix: 1.57 (0.19), residues: 683 sheet: -1.42 (0.43), residues: 119 loop : -2.16 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 62 TYR 0.024 0.002 TYR B 225 PHE 0.041 0.002 PHE B 465 TRP 0.012 0.002 TRP A 653 HIS 0.007 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.27 (10255) covalent geometry : angle 0.75603 / 0.37 (13966) SS BOND : bond 0.00804 / 0.42 ( 5) SS BOND : angle 1.02247 / 0.68 ( 10) hydrogen bonds : bond 0.04314 / 2.96 ( 580) hydrogen bonds : angle 4.79449 / 3.35 ( 1698) link_BETA1-3 : bond 0.00247 / 0.13 ( 1) link_BETA1-3 : angle 1.38985 / 1.17 ( 3) link_BETA1-4 : bond 0.00211 / 0.11 ( 7) link_BETA1-4 : angle 2.19419 / 1.27 ( 21) link_BETA1-6 : bond 0.00750 / 0.39 ( 1) link_BETA1-6 : angle 1.27209 / 1.01 ( 3) link_NAG-ASN : bond 0.00704 / 0.43 ( 11) link_NAG-ASN : angle 2.97065 / 1.97 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 232 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 SER cc_start: 0.8721 (t) cc_final: 0.8470 (p) REVERT: A 95 MET cc_start: 0.8144 (mtp) cc_final: 0.7664 (ttm) REVERT: A 104 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8753 (p) REVERT: A 156 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: A 167 LEU cc_start: 0.9273 (tp) cc_final: 0.8998 (tt) REVERT: A 221 MET cc_start: 0.9334 (mmt) cc_final: 0.9128 (mmt) REVERT: A 305 GLN cc_start: 0.8928 (tp40) cc_final: 0.8676 (tp40) REVERT: A 355 GLN cc_start: 0.8374 (tp40) cc_final: 0.7898 (mm-40) REVERT: A 357 GLU cc_start: 0.8260 (tt0) cc_final: 0.8042 (tt0) REVERT: A 364 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: A 522 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8908 (mp) REVERT: A 587 GLN cc_start: 0.8215 (tp40) cc_final: 0.7724 (pt0) REVERT: A 693 LYS cc_start: 0.8785 (mmtp) cc_final: 0.8452 (mtpp) REVERT: A 695 ASP cc_start: 0.7522 (m-30) cc_final: 0.6694 (t70) REVERT: B 225 TYR cc_start: 0.8605 (m-80) cc_final: 0.7741 (m-80) REVERT: B 233 MET cc_start: 0.8926 (tpt) cc_final: 0.8705 (tpt) REVERT: B 244 TRP cc_start: 0.7037 (OUTLIER) cc_final: 0.5721 (m-90) REVERT: B 381 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7714 (tm) REVERT: B 383 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7986 (tm) REVERT: B 387 ILE cc_start: 0.9197 (mt) cc_final: 0.8981 (mp) REVERT: B 421 THR cc_start: 0.9357 (m) cc_final: 0.9029 (p) REVERT: B 429 LYS cc_start: 0.6021 (OUTLIER) cc_final: 0.4691 (mmtt) REVERT: B 432 LEU cc_start: 0.5272 (OUTLIER) cc_final: 0.4878 (tt) REVERT: B 437 ILE cc_start: 0.7807 (tt) cc_final: 0.7319 (mt) REVERT: B 446 TYR cc_start: 0.8572 (t80) cc_final: 0.8326 (t80) REVERT: B 450 ASP cc_start: 0.7993 (t0) cc_final: 0.7632 (t0) REVERT: B 459 GLN cc_start: 0.8342 (mt0) cc_final: 0.8100 (mt0) REVERT: C 55 ILE cc_start: 0.9034 (mm) cc_final: 0.8723 (tt) REVERT: C 96 LYS cc_start: 0.7429 (mttt) cc_final: 0.7072 (tptt) REVERT: C 109 ARG cc_start: 0.7618 (ttp-170) cc_final: 0.7234 (mtm110) REVERT: C 117 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8303 (mtm) REVERT: C 119 TYR cc_start: 0.8643 (t80) cc_final: 0.8306 (t80) REVERT: C 123 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8845 (tp) REVERT: C 180 ASP cc_start: 0.8391 (t70) cc_final: 0.7894 (t70) REVERT: C 218 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: D 5 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.8230 (mtm-85) outliers start: 80 outliers final: 50 residues processed: 281 average time/residue: 0.0840 time to fit residues: 35.0860 Evaluate side-chains 274 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 212 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 TRP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 0.0270 chunk 21 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 ASN A 478 ASN B 464 GLN C 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106834 restraints weight = 15525.804| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.45 r_work: 0.3074 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10280 Z= 0.165 Angle : 0.708 9.811 14036 Z= 0.343 Chirality : 0.046 0.344 1657 Planarity : 0.004 0.042 1705 Dihedral : 8.814 59.981 1400 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.37 % Favored : 94.38 % Rotamer: Outliers : 6.87 % Allowed : 23.95 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.13 (0.24), residues: 1211 helix: 1.58 (0.19), residues: 681 sheet: -1.51 (0.44), residues: 120 loop : -2.05 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 84 TYR 0.016 0.002 TYR B 225 PHE 0.045 0.002 PHE B 465 TRP 0.012 0.001 TRP A 257 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (10255) covalent geometry : angle 0.69460 / 0.34 (13966) SS BOND : bond 0.00560 / 0.29 ( 5) SS BOND : angle 0.72761 / 0.49 ( 10) hydrogen bonds : bond 0.03983 / 2.71 ( 580) hydrogen bonds : angle 4.68822 / 3.28 ( 1698) link_BETA1-3 : bond 0.00331 / 0.17 ( 1) link_BETA1-3 : angle 1.28741 / 1.09 ( 3) link_BETA1-4 : bond 0.00303 / 0.17 ( 7) link_BETA1-4 : angle 1.91460 / 1.08 ( 21) link_BETA1-6 : bond 0.00943 / 0.50 ( 1) link_BETA1-6 : angle 1.26149 / 1.01 ( 3) link_NAG-ASN : bond 0.00530 / 0.33 ( 11) link_NAG-ASN : angle 2.47944 / 1.67 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 228 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8083 (mtp) cc_final: 0.7473 (ttm) REVERT: A 108 MET cc_start: 0.8529 (tpp) cc_final: 0.8192 (mmm) REVERT: A 156 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: A 167 LEU cc_start: 0.9199 (tp) cc_final: 0.8917 (tt) REVERT: A 305 GLN cc_start: 0.8926 (tp40) cc_final: 0.8661 (tp40) REVERT: A 355 GLN cc_start: 0.8375 (tp40) cc_final: 0.7943 (mm-40) REVERT: A 357 GLU cc_start: 0.8265 (tt0) cc_final: 0.8036 (tt0) REVERT: A 364 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: A 587 GLN cc_start: 0.8213 (tp40) cc_final: 0.7725 (pt0) REVERT: A 662 LEU cc_start: 0.9072 (mp) cc_final: 0.8810 (mp) REVERT: A 677 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.7049 (t80) REVERT: A 695 ASP cc_start: 0.7589 (m-30) cc_final: 0.6826 (t70) REVERT: B 225 TYR cc_start: 0.8518 (m-80) cc_final: 0.7781 (m-80) REVERT: B 244 TRP cc_start: 0.7073 (OUTLIER) cc_final: 0.5973 (m-90) REVERT: B 381 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7665 (tm) REVERT: B 383 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7592 (tm) REVERT: B 387 ILE cc_start: 0.9203 (mt) cc_final: 0.9003 (mp) REVERT: B 421 THR cc_start: 0.9313 (m) cc_final: 0.8950 (p) REVERT: B 429 LYS cc_start: 0.5986 (OUTLIER) cc_final: 0.4668 (mmtt) REVERT: B 432 LEU cc_start: 0.4932 (OUTLIER) cc_final: 0.4584 (tt) REVERT: B 437 ILE cc_start: 0.7436 (tt) cc_final: 0.6976 (mt) REVERT: B 446 TYR cc_start: 0.8473 (t80) cc_final: 0.8231 (t80) REVERT: B 450 ASP cc_start: 0.7950 (t0) cc_final: 0.7603 (t0) REVERT: B 459 GLN cc_start: 0.8174 (mt0) cc_final: 0.7901 (mt0) REVERT: C 48 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8605 (mm) REVERT: C 55 ILE cc_start: 0.8920 (mm) cc_final: 0.8659 (tt) REVERT: C 117 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8189 (mtm) REVERT: C 119 TYR cc_start: 0.8617 (t80) cc_final: 0.8290 (t80) REVERT: C 123 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8895 (tp) REVERT: C 174 TRP cc_start: 0.8863 (m-10) cc_final: 0.8389 (m-10) REVERT: C 180 ASP cc_start: 0.8282 (t70) cc_final: 0.7995 (t70) REVERT: D 5 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.7742 (mtp180) REVERT: D 49 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7086 (mm-30) outliers start: 72 outliers final: 43 residues processed: 273 average time/residue: 0.0790 time to fit residues: 32.3379 Evaluate side-chains 270 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 654 LYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 0.0970 chunk 59 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.129483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105292 restraints weight = 15441.060| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.39 r_work: 0.3079 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 10280 Z= 0.150 Angle : 0.697 10.775 14036 Z= 0.337 Chirality : 0.046 0.350 1657 Planarity : 0.004 0.044 1705 Dihedral : 8.597 59.581 1400 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.95 % Favored : 93.81 % Rotamer: Outliers : 6.20 % Allowed : 25.19 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.20 (0.24), residues: 1211 helix: 1.60 (0.19), residues: 681 sheet: -1.30 (0.45), residues: 122 loop : -1.98 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 84 TYR 0.024 0.002 TYR C 210 PHE 0.047 0.002 PHE B 465 TRP 0.012 0.001 TRP A 653 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (10255) covalent geometry : angle 0.68463 / 0.33 (13966) SS BOND : bond 0.00468 / 0.24 ( 5) SS BOND : angle 0.70477 / 0.46 ( 10) hydrogen bonds : bond 0.03897 / 2.65 ( 580) hydrogen bonds : angle 4.64396 / 3.24 ( 1698) link_BETA1-3 : bond 0.00362 / 0.19 ( 1) link_BETA1-3 : angle 1.25121 / 1.05 ( 3) link_BETA1-4 : bond 0.00283 / 0.15 ( 7) link_BETA1-4 : angle 1.96299 / 1.11 ( 21) link_BETA1-6 : bond 0.00907 / 0.48 ( 1) link_BETA1-6 : angle 1.17215 / 0.94 ( 3) link_NAG-ASN : bond 0.00704 / 0.40 ( 11) link_NAG-ASN : angle 2.35842 / 1.60 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 236 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7967 (mtp) cc_final: 0.7487 (ttm) REVERT: A 108 MET cc_start: 0.8471 (tpp) cc_final: 0.8158 (mmm) REVERT: A 156 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7589 (m-80) REVERT: A 167 LEU cc_start: 0.9189 (tp) cc_final: 0.8925 (tt) REVERT: A 174 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: A 305 GLN cc_start: 0.8903 (tp40) cc_final: 0.8633 (tp40) REVERT: A 355 GLN cc_start: 0.8379 (tp40) cc_final: 0.7941 (mm-40) REVERT: A 357 GLU cc_start: 0.8244 (tt0) cc_final: 0.8029 (tt0) REVERT: A 364 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6998 (tm-30) REVERT: A 436 ILE cc_start: 0.9252 (mt) cc_final: 0.9026 (tt) REVERT: A 522 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8957 (mp) REVERT: A 559 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.7928 (m) REVERT: A 662 LEU cc_start: 0.9055 (mp) cc_final: 0.8779 (mp) REVERT: A 677 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.7044 (t80) REVERT: A 695 ASP cc_start: 0.7562 (m-30) cc_final: 0.6816 (t70) REVERT: B 225 TYR cc_start: 0.8513 (m-80) cc_final: 0.7768 (m-80) REVERT: B 237 PHE cc_start: 0.8318 (m-80) cc_final: 0.7841 (m-80) REVERT: B 244 TRP cc_start: 0.7092 (OUTLIER) cc_final: 0.5976 (m-90) REVERT: B 381 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7679 (tm) REVERT: B 383 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7651 (tm) REVERT: B 421 THR cc_start: 0.9266 (m) cc_final: 0.8796 (p) REVERT: B 429 LYS cc_start: 0.5915 (OUTLIER) cc_final: 0.4568 (mmtm) REVERT: B 432 LEU cc_start: 0.4954 (OUTLIER) cc_final: 0.4622 (tt) REVERT: B 440 THR cc_start: 0.8830 (m) cc_final: 0.8398 (p) REVERT: B 446 TYR cc_start: 0.8442 (t80) cc_final: 0.8171 (t80) REVERT: B 450 ASP cc_start: 0.8075 (t0) cc_final: 0.7721 (t0) REVERT: B 459 GLN cc_start: 0.8263 (mt0) cc_final: 0.8007 (mt0) REVERT: C 48 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8622 (mm) REVERT: C 117 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8291 (mtm) REVERT: C 119 TYR cc_start: 0.8580 (t80) cc_final: 0.8280 (t80) REVERT: C 123 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8893 (tp) REVERT: C 174 TRP cc_start: 0.8914 (m-10) cc_final: 0.8447 (m-10) REVERT: C 180 ASP cc_start: 0.8165 (t70) cc_final: 0.7856 (t70) REVERT: D 5 ARG cc_start: 0.8506 (mtm-85) cc_final: 0.7732 (mtp180) REVERT: D 37 PHE cc_start: 0.8426 (m-80) cc_final: 0.8061 (m-80) outliers start: 65 outliers final: 40 residues processed: 274 average time/residue: 0.0751 time to fit residues: 31.1400 Evaluate side-chains 271 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 654 LYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS C 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.132325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108017 restraints weight = 15459.726| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.49 r_work: 0.3040 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 10280 Z= 0.198 Angle : 0.727 10.012 14036 Z= 0.352 Chirality : 0.048 0.503 1657 Planarity : 0.004 0.043 1705 Dihedral : 8.562 58.815 1400 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.95 % Favored : 93.81 % Rotamer: Outliers : 6.77 % Allowed : 25.00 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.15 (0.24), residues: 1211 helix: 1.54 (0.19), residues: 679 sheet: -1.18 (0.45), residues: 118 loop : -2.01 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 84 TYR 0.022 0.002 TYR B 225 PHE 0.047 0.002 PHE B 465 TRP 0.015 0.001 TRP B 247 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (10255) covalent geometry : angle 0.70856 / 0.35 (13966) SS BOND : bond 0.00665 / 0.34 ( 5) SS BOND : angle 0.87753 / 0.50 ( 10) hydrogen bonds : bond 0.04033 / 2.76 ( 580) hydrogen bonds : angle 4.64076 / 3.24 ( 1698) link_BETA1-3 : bond 0.00255 / 0.13 ( 1) link_BETA1-3 : angle 1.25342 / 1.06 ( 3) link_BETA1-4 : bond 0.00211 / 0.11 ( 7) link_BETA1-4 : angle 1.96311 / 1.12 ( 21) link_BETA1-6 : bond 0.00807 / 0.42 ( 1) link_BETA1-6 : angle 1.20064 / 0.95 ( 3) link_NAG-ASN : bond 0.00702 / 0.42 ( 11) link_NAG-ASN : angle 3.03889 / 1.95 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 217 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8095 (mtp) cc_final: 0.7810 (ttm) REVERT: A 108 MET cc_start: 0.8495 (tpp) cc_final: 0.8231 (mmm) REVERT: A 156 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: A 167 LEU cc_start: 0.9223 (tp) cc_final: 0.8964 (tt) REVERT: A 174 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: A 305 GLN cc_start: 0.8841 (tp40) cc_final: 0.8586 (tp40) REVERT: A 347 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8151 (mmm) REVERT: A 355 GLN cc_start: 0.8422 (tp40) cc_final: 0.7848 (mm-40) REVERT: A 357 GLU cc_start: 0.8218 (tt0) cc_final: 0.7992 (tt0) REVERT: A 364 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6963 (tm-30) REVERT: A 436 ILE cc_start: 0.9193 (mt) cc_final: 0.8939 (tt) REVERT: A 522 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8946 (mp) REVERT: A 559 SER cc_start: 0.8292 (OUTLIER) cc_final: 0.7979 (m) REVERT: A 587 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7627 (mm-40) REVERT: A 662 LEU cc_start: 0.9076 (mp) cc_final: 0.8790 (mp) REVERT: A 677 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.7031 (t80) REVERT: A 695 ASP cc_start: 0.7620 (m-30) cc_final: 0.6853 (t70) REVERT: B 225 TYR cc_start: 0.8560 (m-80) cc_final: 0.7717 (m-80) REVERT: B 237 PHE cc_start: 0.8292 (m-80) cc_final: 0.7848 (m-80) REVERT: B 244 TRP cc_start: 0.7056 (OUTLIER) cc_final: 0.5930 (m-90) REVERT: B 381 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7750 (tm) REVERT: B 421 THR cc_start: 0.9275 (m) cc_final: 0.8906 (p) REVERT: B 429 LYS cc_start: 0.5906 (OUTLIER) cc_final: 0.4630 (mmtm) REVERT: B 432 LEU cc_start: 0.5066 (OUTLIER) cc_final: 0.4754 (tt) REVERT: B 437 ILE cc_start: 0.7390 (tt) cc_final: 0.6915 (mt) REVERT: B 446 TYR cc_start: 0.8608 (t80) cc_final: 0.8251 (t80) REVERT: B 450 ASP cc_start: 0.8118 (t0) cc_final: 0.7753 (t0) REVERT: B 459 GLN cc_start: 0.8293 (mt0) cc_final: 0.8013 (mt0) REVERT: C 48 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8612 (mm) REVERT: C 119 TYR cc_start: 0.8618 (t80) cc_final: 0.8266 (t80) REVERT: C 123 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8911 (tp) REVERT: C 174 TRP cc_start: 0.8927 (m-10) cc_final: 0.8454 (m-10) REVERT: C 180 ASP cc_start: 0.8207 (t70) cc_final: 0.7897 (t70) REVERT: C 218 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: D 5 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8215 (mtm-85) REVERT: D 37 PHE cc_start: 0.8497 (m-80) cc_final: 0.8205 (m-80) REVERT: D 91 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.8092 (t80) outliers start: 71 outliers final: 44 residues processed: 255 average time/residue: 0.0777 time to fit residues: 30.0954 Evaluate side-chains 273 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 214 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 654 LYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 67 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110860 restraints weight = 15240.497| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.33 r_work: 0.3087 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10280 Z= 0.143 Angle : 0.704 12.135 14036 Z= 0.337 Chirality : 0.046 0.362 1657 Planarity : 0.004 0.043 1705 Dihedral : 8.366 58.360 1400 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.70 % Favored : 94.05 % Rotamer: Outliers : 5.82 % Allowed : 26.34 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.22 (0.24), residues: 1211 helix: 1.56 (0.19), residues: 680 sheet: -1.29 (0.44), residues: 122 loop : -1.88 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 84 TYR 0.016 0.001 TYR C 156 PHE 0.051 0.002 PHE B 465 TRP 0.011 0.001 TRP C 209 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (10255) covalent geometry : angle 0.68848 / 0.33 (13966) SS BOND : bond 0.00498 / 0.25 ( 5) SS BOND : angle 0.75770 / 0.43 ( 10) hydrogen bonds : bond 0.03840 / 2.62 ( 580) hydrogen bonds : angle 4.56476 / 3.18 ( 1698) link_BETA1-3 : bond 0.00318 / 0.17 ( 1) link_BETA1-3 : angle 1.19246 / 1.01 ( 3) link_BETA1-4 : bond 0.00295 / 0.16 ( 7) link_BETA1-4 : angle 1.83714 / 1.05 ( 21) link_BETA1-6 : bond 0.00863 / 0.45 ( 1) link_BETA1-6 : angle 1.18847 / 0.96 ( 3) link_NAG-ASN : bond 0.00776 / 0.49 ( 11) link_NAG-ASN : angle 2.76567 / 1.83 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 235 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 THR cc_start: 0.9084 (m) cc_final: 0.8810 (p) REVERT: A 95 MET cc_start: 0.7954 (mtp) cc_final: 0.7650 (ttm) REVERT: A 156 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.7622 (m-80) REVERT: A 167 LEU cc_start: 0.9149 (tp) cc_final: 0.8944 (tt) REVERT: A 305 GLN cc_start: 0.8822 (tp40) cc_final: 0.8545 (tp40) REVERT: A 355 GLN cc_start: 0.8393 (tp40) cc_final: 0.7965 (mm-40) REVERT: A 357 GLU cc_start: 0.8170 (tt0) cc_final: 0.7962 (tt0) REVERT: A 364 GLU cc_start: 0.7685 (tm-30) cc_final: 0.6684 (tm-30) REVERT: A 436 ILE cc_start: 0.9206 (mt) cc_final: 0.8941 (tt) REVERT: A 522 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8959 (mp) REVERT: A 587 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7621 (mm-40) REVERT: A 662 LEU cc_start: 0.9027 (mp) cc_final: 0.8711 (mp) REVERT: A 677 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6963 (t80) REVERT: A 695 ASP cc_start: 0.7563 (m-30) cc_final: 0.6824 (t70) REVERT: B 187 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8490 (mmtm) REVERT: B 225 TYR cc_start: 0.8615 (m-80) cc_final: 0.7916 (m-80) REVERT: B 233 MET cc_start: 0.8791 (tpt) cc_final: 0.8314 (tpt) REVERT: B 237 PHE cc_start: 0.8258 (m-80) cc_final: 0.7707 (m-80) REVERT: B 244 TRP cc_start: 0.7063 (OUTLIER) cc_final: 0.5909 (m-90) REVERT: B 381 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7778 (tm) REVERT: B 421 THR cc_start: 0.9139 (m) cc_final: 0.8868 (p) REVERT: B 429 LYS cc_start: 0.5718 (OUTLIER) cc_final: 0.4484 (mmtm) REVERT: B 432 LEU cc_start: 0.5261 (OUTLIER) cc_final: 0.5013 (tt) REVERT: B 440 THR cc_start: 0.8864 (m) cc_final: 0.8424 (p) REVERT: B 446 TYR cc_start: 0.8616 (t80) cc_final: 0.8266 (t80) REVERT: B 450 ASP cc_start: 0.7997 (t0) cc_final: 0.7652 (t0) REVERT: B 459 GLN cc_start: 0.8015 (mt0) cc_final: 0.7717 (mt0) REVERT: B 464 GLN cc_start: 0.8621 (tt0) cc_final: 0.8414 (tt0) REVERT: C 48 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8621 (mm) REVERT: C 123 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8844 (tp) REVERT: C 174 TRP cc_start: 0.8897 (m-10) cc_final: 0.8344 (m-10) REVERT: C 180 ASP cc_start: 0.8269 (t70) cc_final: 0.7909 (t70) REVERT: C 218 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: D 5 ARG cc_start: 0.8469 (mtm-85) cc_final: 0.8203 (mtm-85) REVERT: D 37 PHE cc_start: 0.8490 (m-80) cc_final: 0.8189 (m-80) outliers start: 61 outliers final: 40 residues processed: 270 average time/residue: 0.0785 time to fit residues: 32.1044 Evaluate side-chains 273 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 51 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 110 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 223 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111154 restraints weight = 15357.018| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.51 r_work: 0.3089 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10280 Z= 0.146 Angle : 0.711 11.878 14036 Z= 0.340 Chirality : 0.047 0.410 1657 Planarity : 0.004 0.043 1705 Dihedral : 8.116 58.074 1394 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.53 % Favored : 94.22 % Rotamer: Outliers : 5.15 % Allowed : 27.96 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.18 (0.24), residues: 1211 helix: 1.49 (0.19), residues: 682 sheet: -1.22 (0.44), residues: 122 loop : -1.85 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 84 TYR 0.016 0.001 TYR B 225 PHE 0.056 0.002 PHE B 465 TRP 0.010 0.001 TRP A 653 HIS 0.005 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (10255) covalent geometry : angle 0.69489 / 0.34 (13966) SS BOND : bond 0.00485 / 0.25 ( 5) SS BOND : angle 0.71534 / 0.42 ( 10) hydrogen bonds : bond 0.03829 / 2.61 ( 580) hydrogen bonds : angle 4.54217 / 3.16 ( 1698) link_BETA1-3 : bond 0.00334 / 0.18 ( 1) link_BETA1-3 : angle 1.19934 / 1.00 ( 3) link_BETA1-4 : bond 0.00252 / 0.13 ( 7) link_BETA1-4 : angle 1.98759 / 1.11 ( 21) link_BETA1-6 : bond 0.00871 / 0.46 ( 1) link_BETA1-6 : angle 1.20261 / 0.98 ( 3) link_NAG-ASN : bond 0.00804 / 0.47 ( 11) link_NAG-ASN : angle 2.74388 / 1.90 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 226 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: A 167 LEU cc_start: 0.9176 (tp) cc_final: 0.8960 (tt) REVERT: A 305 GLN cc_start: 0.8838 (tp40) cc_final: 0.8584 (tp40) REVERT: A 310 GLU cc_start: 0.7661 (tp30) cc_final: 0.7429 (tt0) REVERT: A 355 GLN cc_start: 0.8396 (tp40) cc_final: 0.7916 (mm-40) REVERT: A 357 GLU cc_start: 0.8269 (tt0) cc_final: 0.8023 (tt0) REVERT: A 364 GLU cc_start: 0.7694 (tm-30) cc_final: 0.6637 (tm-30) REVERT: A 436 ILE cc_start: 0.9218 (mt) cc_final: 0.8936 (tt) REVERT: A 522 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8921 (mp) REVERT: A 587 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7651 (mm-40) REVERT: A 662 LEU cc_start: 0.9048 (mp) cc_final: 0.8748 (mp) REVERT: A 677 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6901 (t80) REVERT: A 695 ASP cc_start: 0.7561 (m-30) cc_final: 0.6811 (t70) REVERT: B 187 LYS cc_start: 0.8726 (mmtm) cc_final: 0.8454 (mmtm) REVERT: B 225 TYR cc_start: 0.8599 (m-80) cc_final: 0.7877 (m-80) REVERT: B 233 MET cc_start: 0.8759 (tpt) cc_final: 0.8245 (tpt) REVERT: B 237 PHE cc_start: 0.8226 (m-80) cc_final: 0.7647 (m-80) REVERT: B 244 TRP cc_start: 0.7035 (OUTLIER) cc_final: 0.5965 (m-90) REVERT: B 381 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7777 (tm) REVERT: B 421 THR cc_start: 0.9121 (m) cc_final: 0.8864 (p) REVERT: B 429 LYS cc_start: 0.5636 (OUTLIER) cc_final: 0.4421 (mmtm) REVERT: B 432 LEU cc_start: 0.5213 (OUTLIER) cc_final: 0.4985 (tt) REVERT: B 440 THR cc_start: 0.8823 (m) cc_final: 0.8404 (p) REVERT: B 446 TYR cc_start: 0.8533 (t80) cc_final: 0.8241 (t80) REVERT: B 450 ASP cc_start: 0.8030 (t0) cc_final: 0.7697 (t0) REVERT: B 459 GLN cc_start: 0.8110 (mt0) cc_final: 0.7785 (mt0) REVERT: C 48 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8609 (mm) REVERT: C 123 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8790 (tp) REVERT: C 174 TRP cc_start: 0.8898 (m-10) cc_final: 0.8342 (m-10) REVERT: C 218 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7800 (m-80) REVERT: D 5 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8210 (mtm-85) REVERT: D 37 PHE cc_start: 0.8491 (m-80) cc_final: 0.8198 (m-80) REVERT: D 91 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.8059 (t80) outliers start: 54 outliers final: 40 residues processed: 255 average time/residue: 0.0763 time to fit residues: 29.3858 Evaluate side-chains 269 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 218 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110745 restraints weight = 15563.480| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.49 r_work: 0.3135 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10280 Z= 0.151 Angle : 0.716 11.685 14036 Z= 0.343 Chirality : 0.047 0.416 1657 Planarity : 0.004 0.043 1705 Dihedral : 8.079 57.639 1394 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.53 % Favored : 94.30 % Rotamer: Outliers : 5.15 % Allowed : 28.53 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.15 (0.24), residues: 1211 helix: 1.41 (0.19), residues: 682 sheet: -1.18 (0.44), residues: 122 loop : -1.76 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 84 TYR 0.017 0.001 TYR B 225 PHE 0.049 0.002 PHE B 465 TRP 0.013 0.001 TRP C 209 HIS 0.005 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (10255) covalent geometry : angle 0.70064 / 0.34 (13966) SS BOND : bond 0.00507 / 0.26 ( 5) SS BOND : angle 0.69757 / 0.41 ( 10) hydrogen bonds : bond 0.03816 / 2.61 ( 580) hydrogen bonds : angle 4.57215 / 3.17 ( 1698) link_BETA1-3 : bond 0.00317 / 0.17 ( 1) link_BETA1-3 : angle 1.20708 / 1.01 ( 3) link_BETA1-4 : bond 0.00240 / 0.12 ( 7) link_BETA1-4 : angle 1.90136 / 1.08 ( 21) link_BETA1-6 : bond 0.00859 / 0.45 ( 1) link_BETA1-6 : angle 1.19372 / 0.97 ( 3) link_NAG-ASN : bond 0.00847 / 0.49 ( 11) link_NAG-ASN : angle 2.77096 / 1.94 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2073.04 seconds wall clock time: 36 minutes 27.01 seconds (2187.01 seconds total)