Starting phenix.real_space_refine on Mon Jun 9 09:17:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5a63_3061/06_2025/5a63_3061.cif Found real_map, /net/cci-nas-00/data/ceres_data/5a63_3061/06_2025/5a63_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5a63_3061/06_2025/5a63_3061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5a63_3061/06_2025/5a63_3061.map" model { file = "/net/cci-nas-00/data/ceres_data/5a63_3061/06_2025/5a63_3061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5a63_3061/06_2025/5a63_3061.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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: 6.49, per 1000 atoms: 0.65 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: 3.10 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.15 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: 3.57 Time building geometry restraints manager: 3.57 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 - 24.23: 5567 24.23 - 48.46: 521 48.46 - 72.69: 135 72.69 - 96.92: 36 96.92 - 121.15: 5 Dihedral angle restraints: 6264 sinusoidal: 2700 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 6261 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: 0.310 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.870 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4049 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 : 20.477 121.149 3951 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (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 TRP 0.021 0.002 TRP A 289 HIS 0.007 0.002 HIS A 199 PHE 0.033 0.003 PHE B 386 TYR 0.031 0.003 TYR B 225 ARG 0.009 0.001 ARG A 657 Details of bonding type rmsd link_NAG-ASN : bond 0.14525 ( 11) link_NAG-ASN : angle 9.91942 ( 33) link_BETA1-4 : bond 0.00498 ( 7) link_BETA1-4 : angle 8.10627 ( 21) hydrogen bonds : bond 0.16835 ( 580) hydrogen bonds : angle 6.76479 ( 1698) link_BETA1-6 : bond 0.00688 ( 1) link_BETA1-6 : angle 2.93101 ( 3) SS BOND : bond 0.47461 ( 5) SS BOND : angle 13.39284 ( 10) link_BETA1-3 : bond 0.00373 ( 1) link_BETA1-3 : angle 3.09807 ( 3) covalent geometry : bond 0.00991 (10255) covalent geometry : angle 1.68869 (13966) *********************** 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 : 1.091 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: 0.2244 time to fit residues: 121.6324 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 : 1.111 ------------------------------------------------------------------------------- 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 102 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 163 GLN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.132051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107808 restraints weight = 15287.967| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.46 r_work: 0.3067 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10280 Z= 0.193 Angle : 0.840 11.758 14036 Z= 0.414 Chirality : 0.052 0.370 1657 Planarity : 0.006 0.049 1705 Dihedral : 15.096 104.575 1926 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.87 % Favored : 94.72 % Rotamer: Outliers : 9.26 % Allowed : 17.94 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1211 helix: 2.39 (0.20), residues: 688 sheet: -1.55 (0.44), residues: 118 loop : -2.30 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 257 HIS 0.011 0.002 HIS A 553 PHE 0.040 0.003 PHE B 465 TYR 0.020 0.002 TYR A 569 ARG 0.011 0.001 ARG C 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00680 ( 11) link_NAG-ASN : angle 2.78815 ( 33) link_BETA1-4 : bond 0.00405 ( 7) link_BETA1-4 : angle 2.87077 ( 21) hydrogen bonds : bond 0.04637 ( 580) hydrogen bonds : angle 5.01043 ( 1698) link_BETA1-6 : bond 0.01012 ( 1) link_BETA1-6 : angle 2.86424 ( 3) SS BOND : bond 0.02111 ( 5) SS BOND : angle 1.71533 ( 10) link_BETA1-3 : bond 0.01157 ( 1) link_BETA1-3 : angle 1.81652 ( 3) covalent geometry : bond 0.00424 (10255) covalent geometry : angle 0.82106 (13966) *********************** 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 347 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 250 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8797 (mtt180) cc_final: 0.8330 (mtm110) REVERT: A 65 SER cc_start: 0.9065 (t) cc_final: 0.8731 (p) REVERT: A 69 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8741 (t0) REVERT: A 95 MET cc_start: 0.7971 (mtp) cc_final: 0.7503 (mtp) REVERT: A 104 THR cc_start: 0.9040 (m) cc_final: 0.8751 (p) REVERT: A 111 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8549 (tt) REVERT: A 156 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: A 167 LEU cc_start: 0.9289 (tp) cc_final: 0.8962 (tt) REVERT: A 186 GLU cc_start: 0.8053 (tp30) cc_final: 0.7814 (tp30) REVERT: A 204 ASN cc_start: 0.8054 (m-40) cc_final: 0.7043 (t0) REVERT: A 210 PHE cc_start: 0.8493 (t80) cc_final: 0.8267 (t80) REVERT: A 248 CYS cc_start: 0.6849 (OUTLIER) cc_final: 0.6499 (m) REVERT: A 347 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7934 (mtm) REVERT: A 428 GLN cc_start: 0.8334 (mt0) cc_final: 0.8066 (mt0) REVERT: A 431 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8585 (mp) REVERT: A 464 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8129 (t0) REVERT: A 472 SER cc_start: 0.5836 (OUTLIER) cc_final: 0.5618 (m) REVERT: A 587 GLN cc_start: 0.7724 (tp40) cc_final: 0.7219 (pt0) REVERT: A 646 SER cc_start: 0.9072 (p) cc_final: 0.8660 (t) REVERT: A 656 ILE cc_start: 0.8703 (pp) cc_final: 0.8496 (pp) REVERT: A 688 TYR cc_start: 0.8217 (t80) cc_final: 0.7945 (t80) REVERT: A 693 LYS cc_start: 0.8628 (mmtp) cc_final: 0.8231 (mtpp) REVERT: B 81 HIS cc_start: 0.8282 (t-90) cc_final: 0.7794 (m90) REVERT: B 86 PHE cc_start: 0.8162 (m-10) cc_final: 0.7918 (m-10) REVERT: B 233 MET cc_start: 0.8529 (tpt) cc_final: 0.8153 (tpt) REVERT: B 421 THR cc_start: 0.8910 (m) cc_final: 0.8581 (p) REVERT: B 429 LYS cc_start: 0.5916 (OUTLIER) cc_final: 0.4933 (mmtt) REVERT: B 432 LEU cc_start: 0.5005 (OUTLIER) cc_final: 0.4575 (tt) REVERT: B 437 ILE cc_start: 0.8303 (tt) cc_final: 0.7771 (mt) REVERT: B 446 TYR cc_start: 0.8312 (t80) cc_final: 0.8109 (t80) REVERT: C 96 LYS cc_start: 0.7305 (mttt) cc_final: 0.7025 (tptt) REVERT: C 109 ARG cc_start: 0.7664 (tpm-80) cc_final: 0.7160 (mtm110) REVERT: C 117 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8045 (ttm) REVERT: C 123 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8527 (tp) REVERT: C 180 ASP cc_start: 0.8310 (t70) cc_final: 0.7957 (t70) REVERT: C 218 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7839 (m-80) outliers start: 97 outliers final: 43 residues processed: 312 average time/residue: 0.2025 time to fit residues: 90.1622 Evaluate side-chains 263 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 562 ASN 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 B residue 432 LEU 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 74 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 0.0270 chunk 10 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3526 r_free = 0.3526 target = 0.130009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106252 restraints weight = 15625.661| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.42 r_work: 0.3092 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10280 Z= 0.162 Angle : 0.751 9.872 14036 Z= 0.362 Chirality : 0.047 0.339 1657 Planarity : 0.005 0.046 1705 Dihedral : 12.366 96.363 1861 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.04 % Favored : 94.55 % Rotamer: Outliers : 6.77 % Allowed : 21.76 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1211 helix: 2.11 (0.20), residues: 688 sheet: -1.42 (0.44), residues: 122 loop : -2.04 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 257 HIS 0.006 0.001 HIS A 553 PHE 0.046 0.002 PHE B 465 TYR 0.018 0.002 TYR B 225 ARG 0.006 0.001 ARG C 31 Details of bonding type rmsd link_NAG-ASN : bond 0.00649 ( 11) link_NAG-ASN : angle 2.48707 ( 33) link_BETA1-4 : bond 0.00411 ( 7) link_BETA1-4 : angle 2.47218 ( 21) hydrogen bonds : bond 0.04226 ( 580) hydrogen bonds : angle 4.75055 ( 1698) link_BETA1-6 : bond 0.01419 ( 1) link_BETA1-6 : angle 2.91941 ( 3) SS BOND : bond 0.00525 ( 5) SS BOND : angle 1.61973 ( 10) link_BETA1-3 : bond 0.01036 ( 1) link_BETA1-3 : angle 1.12111 ( 3) covalent geometry : bond 0.00367 (10255) covalent geometry : angle 0.73422 (13966) *********************** 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 309 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 238 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 SER cc_start: 0.8744 (t) cc_final: 0.8372 (p) REVERT: A 82 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8841 (mp) REVERT: A 95 MET cc_start: 0.8037 (mtp) cc_final: 0.7541 (ttm) REVERT: A 104 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8644 (p) REVERT: A 111 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8509 (tt) REVERT: A 167 LEU cc_start: 0.9244 (tp) cc_final: 0.8917 (tt) REVERT: A 204 ASN cc_start: 0.7933 (m-40) cc_final: 0.7078 (t0) REVERT: A 248 CYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6567 (m) REVERT: A 305 GLN cc_start: 0.8725 (tp40) cc_final: 0.8257 (tp40) REVERT: A 347 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.7926 (mtm) REVERT: A 357 GLU cc_start: 0.8479 (tt0) cc_final: 0.8246 (tt0) REVERT: A 428 GLN cc_start: 0.8357 (mt0) cc_final: 0.8153 (mt0) REVERT: A 464 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8323 (t0) REVERT: A 587 GLN cc_start: 0.7754 (tp40) cc_final: 0.7231 (pt0) REVERT: A 688 TYR cc_start: 0.8287 (t80) cc_final: 0.8043 (t80) REVERT: A 693 LYS cc_start: 0.8605 (mmtp) cc_final: 0.8244 (mtpp) REVERT: B 81 HIS cc_start: 0.8201 (t-90) cc_final: 0.7838 (m90) REVERT: B 228 MET cc_start: 0.7846 (mtp) cc_final: 0.7638 (mtp) REVERT: B 233 MET cc_start: 0.8664 (tpt) cc_final: 0.8394 (tpt) REVERT: B 245 THR cc_start: 0.7469 (m) cc_final: 0.7097 (p) REVERT: B 421 THR cc_start: 0.9082 (m) cc_final: 0.8746 (p) REVERT: B 429 LYS cc_start: 0.6291 (OUTLIER) cc_final: 0.4974 (mmtt) REVERT: B 440 THR cc_start: 0.8611 (m) cc_final: 0.8337 (p) REVERT: B 446 TYR cc_start: 0.8380 (t80) cc_final: 0.8113 (t80) REVERT: C 96 LYS cc_start: 0.7244 (mttt) cc_final: 0.6950 (tptt) REVERT: C 109 ARG cc_start: 0.7618 (tpm-80) cc_final: 0.7092 (mtm110) REVERT: C 117 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8113 (mtm) REVERT: C 123 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8650 (tp) REVERT: C 180 ASP cc_start: 0.8314 (t70) cc_final: 0.7966 (t70) REVERT: C 184 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.8083 (mtm-85) REVERT: C 218 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7819 (m-80) outliers start: 71 outliers final: 37 residues processed: 282 average time/residue: 0.2056 time to fit residues: 82.5660 Evaluate side-chains 261 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 104 THR 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 147 VAL 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 338 ILE Chi-restraints excluded: chain A residue 347 MET 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 464 ASN 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 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL 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 241 LEU Chi-restraints excluded: chain B residue 248 LEU 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 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 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 67 TRP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 102 HIS A 200 ASN B 463 HIS D 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.111278 restraints weight = 15318.638| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.52 r_work: 0.3141 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10280 Z= 0.148 Angle : 0.695 10.406 14036 Z= 0.338 Chirality : 0.045 0.276 1657 Planarity : 0.004 0.045 1705 Dihedral : 11.240 88.279 1847 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.95 % Favored : 94.63 % Rotamer: Outliers : 6.97 % Allowed : 22.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1211 helix: 1.97 (0.19), residues: 680 sheet: -1.49 (0.44), residues: 120 loop : -2.01 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 257 HIS 0.005 0.001 HIS A 553 PHE 0.045 0.002 PHE B 465 TYR 0.017 0.002 TYR B 225 ARG 0.004 0.001 ARG D 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 11) link_NAG-ASN : angle 2.15832 ( 33) link_BETA1-4 : bond 0.00388 ( 7) link_BETA1-4 : angle 2.36404 ( 21) hydrogen bonds : bond 0.03961 ( 580) hydrogen bonds : angle 4.62574 ( 1698) link_BETA1-6 : bond 0.01524 ( 1) link_BETA1-6 : angle 3.30959 ( 3) SS BOND : bond 0.00481 ( 5) SS BOND : angle 1.20679 ( 10) link_BETA1-3 : bond 0.00931 ( 1) link_BETA1-3 : angle 1.17918 ( 3) covalent geometry : bond 0.00334 (10255) covalent geometry : angle 0.68015 (13966) *********************** 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 310 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 237 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 SER cc_start: 0.8726 (t) cc_final: 0.8397 (p) REVERT: A 95 MET cc_start: 0.8022 (mtp) cc_final: 0.7503 (ttm) REVERT: A 104 THR cc_start: 0.8991 (m) cc_final: 0.8639 (p) REVERT: A 156 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: A 167 LEU cc_start: 0.9183 (tp) cc_final: 0.8885 (tt) REVERT: A 174 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: A 201 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8090 (mt) REVERT: A 248 CYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6465 (m) REVERT: A 347 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7736 (mmm) REVERT: A 357 GLU cc_start: 0.8474 (tt0) cc_final: 0.8230 (tt0) REVERT: A 428 GLN cc_start: 0.8319 (mt0) cc_final: 0.8070 (mt0) REVERT: A 587 GLN cc_start: 0.8086 (tp40) cc_final: 0.7674 (pt0) REVERT: A 677 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7024 (t80) REVERT: A 688 TYR cc_start: 0.8297 (t80) cc_final: 0.8063 (t80) REVERT: A 693 LYS cc_start: 0.8779 (mmtp) cc_final: 0.8450 (mtpp) REVERT: A 695 ASP cc_start: 0.7363 (m-30) cc_final: 0.6483 (t70) REVERT: B 228 MET cc_start: 0.7856 (mtp) cc_final: 0.7594 (mtp) REVERT: B 233 MET cc_start: 0.8772 (tpt) cc_final: 0.8447 (tpt) REVERT: B 244 TRP cc_start: 0.7075 (OUTLIER) cc_final: 0.5856 (m-90) REVERT: B 245 THR cc_start: 0.7518 (m) cc_final: 0.7112 (p) REVERT: B 387 ILE cc_start: 0.9213 (mt) cc_final: 0.8986 (mp) REVERT: B 421 THR cc_start: 0.9086 (m) cc_final: 0.8789 (p) REVERT: B 429 LYS cc_start: 0.6005 (OUTLIER) cc_final: 0.4635 (mmtt) REVERT: B 446 TYR cc_start: 0.8442 (t80) cc_final: 0.8145 (t80) REVERT: B 450 ASP cc_start: 0.7984 (t0) cc_final: 0.7585 (t0) REVERT: C 96 LYS cc_start: 0.7282 (mttt) cc_final: 0.6957 (tptt) REVERT: C 123 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8766 (tp) REVERT: C 168 ILE cc_start: 0.8167 (mm) cc_final: 0.7950 (mm) REVERT: C 174 TRP cc_start: 0.8829 (m-10) cc_final: 0.8372 (m-10) REVERT: C 180 ASP cc_start: 0.8332 (t70) cc_final: 0.8030 (t70) REVERT: C 184 ARG cc_start: 0.8657 (mmm-85) cc_final: 0.8295 (mtm180) REVERT: C 206 LEU cc_start: 0.8294 (mt) cc_final: 0.8090 (mp) REVERT: C 218 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7755 (m-80) outliers start: 73 outliers final: 43 residues processed: 284 average time/residue: 0.2033 time to fit residues: 83.5140 Evaluate side-chains 268 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 215 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 201 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 312 LEU 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 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 450 ASN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 643 THR 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 172 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 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 C residue 33 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 VAL 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 193 VAL Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 218 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 92 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 102 HIS C 207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.126810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.102757 restraints weight = 15549.396| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.40 r_work: 0.3103 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10280 Z= 0.221 Angle : 0.731 9.302 14036 Z= 0.356 Chirality : 0.048 0.414 1657 Planarity : 0.004 0.046 1705 Dihedral : 10.409 77.773 1835 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.70 % Favored : 93.97 % Rotamer: Outliers : 7.82 % Allowed : 21.76 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.24), residues: 1211 helix: 1.74 (0.19), residues: 681 sheet: -1.47 (0.43), residues: 116 loop : -2.09 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 85 HIS 0.006 0.001 HIS A 553 PHE 0.043 0.002 PHE B 465 TYR 0.024 0.002 TYR B 225 ARG 0.004 0.001 ARG A 429 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 11) link_NAG-ASN : angle 2.70947 ( 33) link_BETA1-4 : bond 0.00287 ( 7) link_BETA1-4 : angle 2.24345 ( 21) hydrogen bonds : bond 0.04152 ( 580) hydrogen bonds : angle 4.68665 ( 1698) link_BETA1-6 : bond 0.01598 ( 1) link_BETA1-6 : angle 3.60206 ( 3) SS BOND : bond 0.00643 ( 5) SS BOND : angle 1.25475 ( 10) link_BETA1-3 : bond 0.00800 ( 1) link_BETA1-3 : angle 1.62617 ( 3) covalent geometry : bond 0.00512 (10255) covalent geometry : angle 0.71297 (13966) *********************** 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 304 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 222 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 SER cc_start: 0.8587 (t) cc_final: 0.8342 (p) REVERT: A 95 MET cc_start: 0.8047 (mtp) cc_final: 0.7584 (ttm) REVERT: A 104 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8720 (p) REVERT: A 156 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: A 167 LEU cc_start: 0.9273 (tp) cc_final: 0.9033 (tt) REVERT: A 355 GLN cc_start: 0.8376 (tp40) cc_final: 0.7993 (mm-40) REVERT: A 522 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8980 (mp) REVERT: A 587 GLN cc_start: 0.8182 (tp40) cc_final: 0.7699 (pt0) REVERT: A 693 LYS cc_start: 0.8830 (mmtp) cc_final: 0.8532 (mtpp) REVERT: A 695 ASP cc_start: 0.7470 (m-30) cc_final: 0.6681 (t70) REVERT: B 91 LEU cc_start: 0.8732 (mp) cc_final: 0.8435 (mt) REVERT: B 225 TYR cc_start: 0.8587 (m-80) cc_final: 0.7723 (m-80) REVERT: B 228 MET cc_start: 0.7943 (mtp) cc_final: 0.7649 (mtp) REVERT: B 233 MET cc_start: 0.8903 (tpt) cc_final: 0.8656 (tpt) REVERT: B 244 TRP cc_start: 0.7100 (OUTLIER) cc_final: 0.5963 (m-90) REVERT: B 387 ILE cc_start: 0.9271 (mt) cc_final: 0.9060 (mp) REVERT: B 421 THR cc_start: 0.9188 (m) cc_final: 0.8873 (p) REVERT: B 429 LYS cc_start: 0.6022 (OUTLIER) cc_final: 0.4675 (mmtt) REVERT: B 446 TYR cc_start: 0.8487 (t80) cc_final: 0.8240 (t80) REVERT: B 450 ASP cc_start: 0.7981 (t0) cc_final: 0.7592 (t0) REVERT: C 96 LYS cc_start: 0.7457 (mttt) cc_final: 0.7123 (tptt) REVERT: C 123 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8822 (tp) REVERT: C 174 TRP cc_start: 0.8819 (m-10) cc_final: 0.8384 (m-10) REVERT: C 180 ASP cc_start: 0.8374 (t70) cc_final: 0.7985 (t70) REVERT: C 184 ARG cc_start: 0.8670 (mmm-85) cc_final: 0.8396 (mtm-85) REVERT: C 218 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7925 (m-80) REVERT: D 19 TYR cc_start: 0.8046 (t80) cc_final: 0.7826 (t80) REVERT: D 38 PHE cc_start: 0.7514 (t80) cc_final: 0.7302 (t80) outliers start: 82 outliers final: 56 residues processed: 278 average time/residue: 0.2341 time to fit residues: 95.5147 Evaluate side-chains 270 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 207 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 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 297 SER Chi-restraints excluded: chain A residue 338 ILE 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 494 LEU 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 643 THR 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 200 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 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 422 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 56 LEU 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 164 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain D residue 60 SER 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 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 17 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 462 ASN C 207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.105727 restraints weight = 15531.511| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.51 r_work: 0.3098 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10280 Z= 0.170 Angle : 0.699 9.826 14036 Z= 0.338 Chirality : 0.046 0.400 1657 Planarity : 0.004 0.041 1705 Dihedral : 9.712 71.724 1829 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.28 % Favored : 94.47 % Rotamer: Outliers : 6.49 % Allowed : 24.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1211 helix: 1.70 (0.19), residues: 678 sheet: -1.50 (0.43), residues: 119 loop : -2.02 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 247 HIS 0.006 0.001 HIS A 553 PHE 0.046 0.002 PHE B 465 TYR 0.019 0.002 TYR B 225 ARG 0.005 0.000 ARG D 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 11) link_NAG-ASN : angle 2.46206 ( 33) link_BETA1-4 : bond 0.00339 ( 7) link_BETA1-4 : angle 2.17189 ( 21) hydrogen bonds : bond 0.03922 ( 580) hydrogen bonds : angle 4.62407 ( 1698) link_BETA1-6 : bond 0.01712 ( 1) link_BETA1-6 : angle 3.92742 ( 3) SS BOND : bond 0.00532 ( 5) SS BOND : angle 0.68389 ( 10) link_BETA1-3 : bond 0.00834 ( 1) link_BETA1-3 : angle 1.54708 ( 3) covalent geometry : bond 0.00394 (10255) covalent geometry : angle 0.68218 (13966) *********************** 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 290 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8057 (mtp) cc_final: 0.7676 (ttm) REVERT: A 156 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: A 167 LEU cc_start: 0.9261 (tp) cc_final: 0.8999 (tt) REVERT: A 201 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8036 (mt) REVERT: A 355 GLN cc_start: 0.8344 (tp40) cc_final: 0.7917 (mm-40) REVERT: A 587 GLN cc_start: 0.8231 (tp40) cc_final: 0.7735 (pt0) REVERT: A 656 ILE cc_start: 0.8538 (pp) cc_final: 0.8164 (mt) REVERT: A 677 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.7051 (t80) REVERT: A 695 ASP cc_start: 0.7455 (m-30) cc_final: 0.6697 (t70) REVERT: B 225 TYR cc_start: 0.8509 (m-80) cc_final: 0.7646 (m-80) REVERT: B 228 MET cc_start: 0.7711 (mtp) cc_final: 0.7349 (mtp) REVERT: B 244 TRP cc_start: 0.7075 (OUTLIER) cc_final: 0.5950 (m-90) REVERT: B 421 THR cc_start: 0.9341 (m) cc_final: 0.9038 (p) REVERT: B 429 LYS cc_start: 0.5979 (OUTLIER) cc_final: 0.4640 (mmtt) REVERT: B 440 THR cc_start: 0.8623 (m) cc_final: 0.8313 (p) REVERT: B 450 ASP cc_start: 0.8006 (t0) cc_final: 0.7555 (t0) REVERT: B 454 GLN cc_start: 0.8513 (tp40) cc_final: 0.8106 (tp-100) REVERT: C 96 LYS cc_start: 0.7422 (mttt) cc_final: 0.7063 (tptt) REVERT: C 123 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8800 (tp) REVERT: C 174 TRP cc_start: 0.8774 (m-10) cc_final: 0.8242 (m-10) REVERT: C 180 ASP cc_start: 0.8380 (t70) cc_final: 0.7746 (t70) REVERT: C 184 ARG cc_start: 0.8716 (mmm-85) cc_final: 0.8444 (mtm-85) REVERT: D 38 PHE cc_start: 0.7380 (t80) cc_final: 0.7126 (t80) outliers start: 68 outliers final: 48 residues processed: 266 average time/residue: 0.1888 time to fit residues: 73.5653 Evaluate side-chains 263 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 201 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 338 ILE 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 450 ASN 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 643 THR 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 172 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 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 422 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 56 LEU 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 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 76 THR 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 71 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 9 optimal weight: 0.0060 chunk 81 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 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 = 0.3539 r_free = 0.3539 target = 0.130768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106427 restraints weight = 15672.481| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.52 r_work: 0.3046 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10280 Z= 0.165 Angle : 0.709 10.288 14036 Z= 0.341 Chirality : 0.047 0.498 1657 Planarity : 0.004 0.041 1705 Dihedral : 9.355 71.268 1829 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.95 % Favored : 93.81 % Rotamer: Outliers : 6.39 % Allowed : 26.81 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1211 helix: 1.65 (0.19), residues: 680 sheet: -1.36 (0.44), residues: 116 loop : -2.00 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 67 HIS 0.005 0.001 HIS A 553 PHE 0.048 0.002 PHE B 465 TYR 0.017 0.001 TYR B 225 ARG 0.004 0.000 ARG D 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 11) link_NAG-ASN : angle 2.96062 ( 33) link_BETA1-4 : bond 0.00358 ( 7) link_BETA1-4 : angle 2.12248 ( 21) hydrogen bonds : bond 0.03902 ( 580) hydrogen bonds : angle 4.63073 ( 1698) link_BETA1-6 : bond 0.01657 ( 1) link_BETA1-6 : angle 3.70082 ( 3) SS BOND : bond 0.01150 ( 5) SS BOND : angle 0.64198 ( 10) link_BETA1-3 : bond 0.00752 ( 1) link_BETA1-3 : angle 1.63343 ( 3) covalent geometry : bond 0.00385 (10255) covalent geometry : angle 0.68850 (13966) *********************** 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 291 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 224 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8048 (mtp) cc_final: 0.7692 (ttm) REVERT: A 156 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: A 167 LEU cc_start: 0.9218 (tp) cc_final: 0.8949 (tt) REVERT: A 201 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8011 (mt) REVERT: A 355 GLN cc_start: 0.8420 (tp40) cc_final: 0.7966 (mm-40) REVERT: A 436 ILE cc_start: 0.9194 (mt) cc_final: 0.8966 (tt) REVERT: A 559 SER cc_start: 0.8194 (OUTLIER) cc_final: 0.7898 (m) REVERT: A 656 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8177 (mt) REVERT: A 677 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.7105 (t80) REVERT: A 695 ASP cc_start: 0.7439 (m-30) cc_final: 0.6719 (t70) REVERT: B 91 LEU cc_start: 0.8675 (mp) cc_final: 0.8432 (mt) REVERT: B 225 TYR cc_start: 0.8462 (m-80) cc_final: 0.7605 (m-80) REVERT: B 228 MET cc_start: 0.7765 (mtp) cc_final: 0.7356 (mtp) REVERT: B 237 PHE cc_start: 0.8307 (m-80) cc_final: 0.7840 (m-80) REVERT: B 244 TRP cc_start: 0.7109 (OUTLIER) cc_final: 0.5975 (m-90) REVERT: B 421 THR cc_start: 0.9306 (m) cc_final: 0.8968 (p) REVERT: B 429 LYS cc_start: 0.5906 (OUTLIER) cc_final: 0.4573 (mmtm) REVERT: B 432 LEU cc_start: 0.4818 (OUTLIER) cc_final: 0.4432 (tt) REVERT: B 446 TYR cc_start: 0.8532 (t80) cc_final: 0.8264 (t80) REVERT: B 450 ASP cc_start: 0.8144 (t0) cc_final: 0.7762 (t0) REVERT: C 96 LYS cc_start: 0.7372 (mttt) cc_final: 0.6997 (tptt) REVERT: C 123 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8789 (tp) REVERT: C 174 TRP cc_start: 0.8899 (m-10) cc_final: 0.8338 (m-10) REVERT: C 180 ASP cc_start: 0.8283 (t70) cc_final: 0.7889 (t70) REVERT: C 184 ARG cc_start: 0.8751 (mmm-85) cc_final: 0.8469 (mtm-85) REVERT: D 37 PHE cc_start: 0.8424 (m-80) cc_final: 0.8110 (m-80) outliers start: 67 outliers final: 47 residues processed: 269 average time/residue: 0.2109 time to fit residues: 82.8188 Evaluate side-chains 267 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 211 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 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 201 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 338 ILE 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 450 ASN Chi-restraints excluded: chain A residue 509 ASP 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 631 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 656 ILE 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 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 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 422 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 50 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 56 LEU 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 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 76 THR 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 65 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3554 r_free = 0.3554 target = 0.131977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107684 restraints weight = 15593.515| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.49 r_work: 0.3054 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 10280 Z= 0.193 Angle : 0.717 9.405 14036 Z= 0.347 Chirality : 0.047 0.367 1657 Planarity : 0.004 0.040 1705 Dihedral : 9.290 70.475 1829 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.86 % Favored : 93.89 % Rotamer: Outliers : 6.58 % Allowed : 27.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1211 helix: 1.59 (0.19), residues: 680 sheet: -1.30 (0.43), residues: 119 loop : -2.04 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 85 HIS 0.006 0.001 HIS A 553 PHE 0.051 0.002 PHE B 465 TYR 0.021 0.002 TYR B 225 ARG 0.006 0.000 ARG D 84 Details of bonding type rmsd link_NAG-ASN : bond 0.01049 ( 11) link_NAG-ASN : angle 2.96077 ( 33) link_BETA1-4 : bond 0.00379 ( 7) link_BETA1-4 : angle 2.02928 ( 21) hydrogen bonds : bond 0.03992 ( 580) hydrogen bonds : angle 4.63544 ( 1698) link_BETA1-6 : bond 0.01259 ( 1) link_BETA1-6 : angle 3.17980 ( 3) SS BOND : bond 0.00598 ( 5) SS BOND : angle 0.65445 ( 10) link_BETA1-3 : bond 0.00818 ( 1) link_BETA1-3 : angle 1.85749 ( 3) covalent geometry : bond 0.00456 (10255) covalent geometry : angle 0.69750 (13966) *********************** 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 280 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 211 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: A 95 MET cc_start: 0.8135 (mtp) cc_final: 0.7710 (ttm) REVERT: A 156 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.7607 (m-80) REVERT: A 167 LEU cc_start: 0.9232 (tp) cc_final: 0.8960 (tt) REVERT: A 347 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8215 (mmm) REVERT: A 355 GLN cc_start: 0.8429 (tp40) cc_final: 0.7875 (mm-40) REVERT: A 436 ILE cc_start: 0.9150 (mt) cc_final: 0.8918 (tt) REVERT: A 522 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8972 (mp) REVERT: A 559 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.7985 (m) REVERT: A 587 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7611 (mm-40) REVERT: A 656 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8203 (mt) REVERT: A 695 ASP cc_start: 0.7534 (m-30) cc_final: 0.6835 (t70) REVERT: B 91 LEU cc_start: 0.8714 (mp) cc_final: 0.8423 (mt) REVERT: B 225 TYR cc_start: 0.8520 (m-80) cc_final: 0.7669 (m-80) REVERT: B 228 MET cc_start: 0.7790 (mtp) cc_final: 0.7379 (mtp) REVERT: B 237 PHE cc_start: 0.8332 (m-80) cc_final: 0.7928 (m-80) REVERT: B 244 TRP cc_start: 0.7112 (OUTLIER) cc_final: 0.5956 (m-90) REVERT: B 421 THR cc_start: 0.9214 (m) cc_final: 0.8895 (p) REVERT: B 429 LYS cc_start: 0.5931 (OUTLIER) cc_final: 0.4645 (mmtm) REVERT: B 432 LEU cc_start: 0.4959 (OUTLIER) cc_final: 0.4600 (tt) REVERT: B 446 TYR cc_start: 0.8494 (t80) cc_final: 0.8238 (t80) REVERT: B 450 ASP cc_start: 0.8106 (t0) cc_final: 0.7714 (t0) REVERT: C 123 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8803 (tp) REVERT: C 174 TRP cc_start: 0.8915 (m-10) cc_final: 0.8422 (m-10) REVERT: C 180 ASP cc_start: 0.8204 (t70) cc_final: 0.7780 (t70) REVERT: C 184 ARG cc_start: 0.8745 (mmm-85) cc_final: 0.8463 (mtm-85) outliers start: 69 outliers final: 52 residues processed: 257 average time/residue: 0.2261 time to fit residues: 85.9225 Evaluate side-chains 270 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 208 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 94 TYR Chi-restraints excluded: chain A residue 107 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 297 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 347 MET 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 450 ASN 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 631 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 656 ILE 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 174 LEU Chi-restraints excluded: chain B residue 180 ILE 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 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 422 LEU 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 33 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 93 LEU 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 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 69 ILE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 88 LEU 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 113 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN A 516 GLN C 207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107017 restraints weight = 15513.686| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.50 r_work: 0.3071 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 10280 Z= 0.211 Angle : 0.726 9.790 14036 Z= 0.351 Chirality : 0.047 0.440 1657 Planarity : 0.004 0.042 1705 Dihedral : 9.263 69.767 1829 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.03 % Favored : 93.81 % Rotamer: Outliers : 6.87 % Allowed : 26.91 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.24), residues: 1211 helix: 1.49 (0.19), residues: 680 sheet: -1.01 (0.46), residues: 116 loop : -2.02 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 85 HIS 0.007 0.001 HIS A 553 PHE 0.049 0.002 PHE B 465 TYR 0.023 0.002 TYR B 225 ARG 0.005 0.000 ARG D 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00965 ( 11) link_NAG-ASN : angle 3.09528 ( 33) link_BETA1-4 : bond 0.00346 ( 7) link_BETA1-4 : angle 2.11013 ( 21) hydrogen bonds : bond 0.04048 ( 580) hydrogen bonds : angle 4.66790 ( 1698) link_BETA1-6 : bond 0.00968 ( 1) link_BETA1-6 : angle 2.63391 ( 3) SS BOND : bond 0.00624 ( 5) SS BOND : angle 0.72428 ( 10) link_BETA1-3 : bond 0.00696 ( 1) link_BETA1-3 : angle 1.83964 ( 3) covalent geometry : bond 0.00497 (10255) covalent geometry : angle 0.70510 (13966) *********************** 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 287 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 215 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.7703 (m-80) REVERT: A 95 MET cc_start: 0.8101 (mtp) cc_final: 0.7679 (ttm) REVERT: A 156 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7538 (m-80) REVERT: A 167 LEU cc_start: 0.9245 (tp) cc_final: 0.8997 (tt) REVERT: A 305 GLN cc_start: 0.8836 (tt0) cc_final: 0.8589 (tt0) REVERT: A 347 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8084 (mmm) REVERT: A 355 GLN cc_start: 0.8442 (tp40) cc_final: 0.7875 (mm-40) REVERT: A 522 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8966 (mp) REVERT: A 559 SER cc_start: 0.8310 (OUTLIER) cc_final: 0.8091 (m) REVERT: A 587 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7650 (mm-40) REVERT: A 656 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8140 (mt) REVERT: A 677 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.7039 (t80) REVERT: A 695 ASP cc_start: 0.7523 (m-30) cc_final: 0.6834 (t70) REVERT: B 91 LEU cc_start: 0.8765 (mp) cc_final: 0.8460 (mt) REVERT: B 225 TYR cc_start: 0.8559 (m-80) cc_final: 0.7722 (m-80) REVERT: B 233 MET cc_start: 0.8928 (tpt) cc_final: 0.8438 (tpt) REVERT: B 237 PHE cc_start: 0.8284 (m-80) cc_final: 0.7846 (m-80) REVERT: B 244 TRP cc_start: 0.7118 (OUTLIER) cc_final: 0.5952 (m-90) REVERT: B 421 THR cc_start: 0.9223 (m) cc_final: 0.8891 (p) REVERT: B 429 LYS cc_start: 0.5804 (OUTLIER) cc_final: 0.4482 (mmtm) REVERT: B 432 LEU cc_start: 0.5200 (OUTLIER) cc_final: 0.4937 (tt) REVERT: B 437 ILE cc_start: 0.7413 (tt) cc_final: 0.6931 (mt) REVERT: B 446 TYR cc_start: 0.8472 (t80) cc_final: 0.8235 (t80) REVERT: B 450 ASP cc_start: 0.8023 (t0) cc_final: 0.7576 (t0) REVERT: C 48 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8609 (mm) REVERT: C 123 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8867 (tp) REVERT: C 180 ASP cc_start: 0.8234 (t70) cc_final: 0.7813 (t70) REVERT: C 184 ARG cc_start: 0.8737 (mmm-85) cc_final: 0.8457 (mtm-85) outliers start: 72 outliers final: 50 residues processed: 262 average time/residue: 0.2224 time to fit residues: 85.9611 Evaluate side-chains 269 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 207 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 107 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 297 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 347 MET 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 450 ASN 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 631 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 656 ILE 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 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 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 422 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 24 THR 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 56 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 93 LEU 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 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 76 THR 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 5 optimal weight: 0.1980 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN C 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108234 restraints weight = 15380.770| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.49 r_work: 0.3031 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 10280 Z= 0.193 Angle : 0.719 10.835 14036 Z= 0.348 Chirality : 0.047 0.450 1657 Planarity : 0.004 0.041 1705 Dihedral : 9.203 69.185 1829 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.78 % Favored : 94.05 % Rotamer: Outliers : 6.30 % Allowed : 27.96 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1211 helix: 1.47 (0.19), residues: 682 sheet: -1.12 (0.46), residues: 114 loop : -1.97 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 209 HIS 0.006 0.001 HIS A 553 PHE 0.054 0.002 PHE B 465 TYR 0.022 0.002 TYR B 225 ARG 0.005 0.000 ARG D 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00907 ( 11) link_NAG-ASN : angle 3.25573 ( 33) link_BETA1-4 : bond 0.00345 ( 7) link_BETA1-4 : angle 2.03699 ( 21) hydrogen bonds : bond 0.03971 ( 580) hydrogen bonds : angle 4.65181 ( 1698) link_BETA1-6 : bond 0.00837 ( 1) link_BETA1-6 : angle 2.25592 ( 3) SS BOND : bond 0.00584 ( 5) SS BOND : angle 0.70664 ( 10) link_BETA1-3 : bond 0.00706 ( 1) link_BETA1-3 : angle 1.72869 ( 3) covalent geometry : bond 0.00456 (10255) covalent geometry : angle 0.69759 (13966) ********************** 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 281 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 215 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: A 95 MET cc_start: 0.8121 (mtp) cc_final: 0.7659 (ttm) REVERT: A 156 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7581 (m-80) REVERT: A 167 LEU cc_start: 0.9229 (tp) cc_final: 0.8968 (tt) REVERT: A 347 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8132 (mmm) REVERT: A 355 GLN cc_start: 0.8467 (tp40) cc_final: 0.7825 (mm-40) REVERT: A 522 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8968 (mp) REVERT: A 559 SER cc_start: 0.8308 (OUTLIER) cc_final: 0.8035 (t) REVERT: A 656 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8145 (mt) REVERT: A 677 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.7056 (t80) REVERT: A 695 ASP cc_start: 0.7524 (m-30) cc_final: 0.6831 (t70) REVERT: B 187 LYS cc_start: 0.8715 (mmtm) cc_final: 0.8437 (mmtm) REVERT: B 225 TYR cc_start: 0.8530 (m-80) cc_final: 0.7694 (m-80) REVERT: B 233 MET cc_start: 0.8893 (tpt) cc_final: 0.8412 (tpt) REVERT: B 237 PHE cc_start: 0.8300 (m-80) cc_final: 0.7885 (m-80) REVERT: B 244 TRP cc_start: 0.7098 (OUTLIER) cc_final: 0.5921 (m-90) REVERT: B 421 THR cc_start: 0.9216 (m) cc_final: 0.8872 (p) REVERT: B 429 LYS cc_start: 0.5766 (OUTLIER) cc_final: 0.4474 (mmtm) REVERT: B 432 LEU cc_start: 0.5246 (OUTLIER) cc_final: 0.5000 (tt) REVERT: B 437 ILE cc_start: 0.7368 (tt) cc_final: 0.6884 (mt) REVERT: B 446 TYR cc_start: 0.8464 (t80) cc_final: 0.8237 (t80) REVERT: B 450 ASP cc_start: 0.8057 (t0) cc_final: 0.7629 (t0) REVERT: C 48 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8589 (mm) REVERT: C 123 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8813 (tp) REVERT: C 180 ASP cc_start: 0.8232 (t70) cc_final: 0.7817 (t70) REVERT: C 184 ARG cc_start: 0.8765 (mmm-85) cc_final: 0.8463 (mtm-85) REVERT: C 210 TYR cc_start: 0.8891 (m-80) cc_final: 0.8588 (m-80) outliers start: 66 outliers final: 49 residues processed: 258 average time/residue: 0.1844 time to fit residues: 70.0903 Evaluate side-chains 268 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 207 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 107 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 297 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 347 MET 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 450 ASN 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 631 LEU Chi-restraints excluded: chain A residue 656 ILE 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 188 THR 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 422 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 24 THR 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 56 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 93 LEU 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 231 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 0.0050 chunk 105 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.106665 restraints weight = 15551.321| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.51 r_work: 0.3017 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 10280 Z= 0.212 Angle : 0.728 10.909 14036 Z= 0.354 Chirality : 0.047 0.487 1657 Planarity : 0.004 0.042 1705 Dihedral : 9.168 68.143 1829 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.11 % Favored : 93.72 % Rotamer: Outliers : 6.39 % Allowed : 27.96 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1211 helix: 1.40 (0.19), residues: 682 sheet: -1.18 (0.46), residues: 114 loop : -1.92 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 85 HIS 0.006 0.001 HIS A 553 PHE 0.053 0.002 PHE B 465 TYR 0.023 0.002 TYR B 225 ARG 0.005 0.000 ARG D 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00836 ( 11) link_NAG-ASN : angle 3.33077 ( 33) link_BETA1-4 : bond 0.00347 ( 7) link_BETA1-4 : angle 2.00647 ( 21) hydrogen bonds : bond 0.04034 ( 580) hydrogen bonds : angle 4.65594 ( 1698) link_BETA1-6 : bond 0.00751 ( 1) link_BETA1-6 : angle 2.06432 ( 3) SS BOND : bond 0.00618 ( 5) SS BOND : angle 0.78502 ( 10) link_BETA1-3 : bond 0.00647 ( 1) link_BETA1-3 : angle 1.77312 ( 3) covalent geometry : bond 0.00502 (10255) covalent geometry : angle 0.70621 (13966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4833.84 seconds wall clock time: 86 minutes 27.29 seconds (5187.29 seconds total)