Starting phenix.real_space_refine on Wed Sep 17 18:40:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5a63_3061/09_2025/5a63_3061.cif Found real_map, /net/cci-nas-00/data/ceres_data/5a63_3061/09_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_3061/09_2025/5a63_3061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5a63_3061/09_2025/5a63_3061.map" model { file = "/net/cci-nas-00/data/ceres_data/5a63_3061/09_2025/5a63_3061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5a63_3061/09_2025/5a63_3061.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 35 5.16 5 C 6536 2.51 5 N 1589 2.21 5 O 1841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10003 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5222 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 37, 'TRANS': 627} Chain: "B" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1702 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 6, 'TRANS': 208} Chain breaks: 2 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 850 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 2.45, per 1000 atoms: 0.24 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: 1.19 Conformation dependent library (CDL) restraints added in 381.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2298 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 6 sheets defined 60.9% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 34 through 40 removed outlier: 3.949A pdb=" N ARG A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.515A pdb=" N LEU A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.558A pdb=" N MET A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.787A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.621A pdb=" N CYS A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 removed outlier: 4.047A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.665A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 434 removed outlier: 4.147A pdb=" N ALA A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 474 through 479 removed outlier: 4.239A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 503 Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.610A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 Processing helix chain 'A' and resid 541 through 546 removed outlier: 3.810A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.756A pdb=" N TYR A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 567 " --> pdb=" O THR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 665 through 693 Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'B' and resid 78 through 104 Proline residue: B 88 - end of helix removed outlier: 3.671A pdb=" N SER B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 108 Processing helix chain 'B' and resid 167 through 190 removed outlier: 4.219A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 241 Processing helix chain 'B' and resid 242 through 260 removed outlier: 3.544A pdb=" N ALA B 251 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 399 Processing helix chain 'B' and resid 404 through 428 Processing helix chain 'B' and resid 435 through 452 Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.288A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 24 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 28 through 61 Processing helix chain 'C' and resid 64 through 103 removed outlier: 3.851A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 142 removed outlier: 3.553A pdb=" N TYR C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 141 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.500A pdb=" N THR C 172 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 206 removed outlier: 3.786A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 232 removed outlier: 4.074A pdb=" N LEU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.651A pdb=" N LEU C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 removed outlier: 3.761A pdb=" N ARG D 5 " --> pdb=" O ASN D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 22 Processing helix chain 'D' and resid 26 through 36 Processing helix chain 'D' and resid 37 through 44 Processing helix chain 'D' and resid 49 through 85 removed outlier: 3.597A pdb=" N TRP D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) Proline residue: D 83 - end of helix Processing helix chain 'D' and resid 86 through 92 removed outlier: 3.813A pdb=" N ASP D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 41 through 44 removed outlier: 4.633A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 13.686A pdb=" N VAL A 75 " --> pdb=" O PRO A 211 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AC, first strand: chain 'A' and resid 175 through 176 Processing sheet with id=AD, first strand: chain 'A' and resid 412 through 414 removed outlier: 7.400A pdb=" N VAL A 277 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE A 362 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA A 279 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A 364 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG A 281 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N GLY A 366 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A 253 " --> pdb=" O ALA A 630 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.091A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.858A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1698 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.43 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: 0.530 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.380 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.480 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.22), residues: 1211 helix: 1.34 (0.17), residues: 672 sheet: -1.51 (0.48), residues: 113 loop : -2.13 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 657 TYR 0.031 0.003 TYR B 225 PHE 0.033 0.003 PHE B 386 TRP 0.021 0.002 TRP A 289 HIS 0.007 0.002 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00991 (10255) covalent geometry : angle 1.68869 (13966) SS BOND : bond 0.47461 ( 5) SS BOND : angle 13.39284 ( 10) hydrogen bonds : bond 0.16835 ( 580) hydrogen bonds : angle 6.76479 ( 1698) link_BETA1-3 : bond 0.00373 ( 1) link_BETA1-3 : angle 3.09807 ( 3) link_BETA1-4 : bond 0.00498 ( 7) link_BETA1-4 : angle 8.10627 ( 21) link_BETA1-6 : bond 0.00688 ( 1) link_BETA1-6 : angle 2.93101 ( 3) link_NAG-ASN : bond 0.14525 ( 11) link_NAG-ASN : angle 9.91942 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 299 time to evaluate : 0.286 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: 0.1037 time to fit residues: 56.6399 Evaluate side-chains 265 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 208 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 429 ARG Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 94 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 150 ASN A 163 GLN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN A 305 GLN A 313 GLN A 367 GLN A 418 GLN A 428 GLN A 449 HIS ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN A 587 GLN A 606 GLN B 464 GLN C 136 ASN C 207 ASN D 79 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.134012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109939 restraints weight = 15309.272| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.43 r_work: 0.3083 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10280 Z= 0.198 Angle : 0.844 11.988 14036 Z= 0.416 Chirality : 0.052 0.372 1657 Planarity : 0.006 0.049 1705 Dihedral : 15.063 104.154 1926 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.79 % Favored : 94.72 % Rotamer: Outliers : 9.35 % Allowed : 18.03 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.25), residues: 1211 helix: 2.36 (0.20), residues: 687 sheet: -1.57 (0.44), residues: 118 loop : -2.26 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 62 TYR 0.020 0.002 TYR B 225 PHE 0.040 0.003 PHE B 465 TRP 0.029 0.002 TRP A 257 HIS 0.011 0.002 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00443 (10255) covalent geometry : angle 0.82520 (13966) SS BOND : bond 0.01172 ( 5) SS BOND : angle 1.48695 ( 10) hydrogen bonds : bond 0.04649 ( 580) hydrogen bonds : angle 5.02030 ( 1698) link_BETA1-3 : bond 0.00800 ( 1) link_BETA1-3 : angle 1.68551 ( 3) link_BETA1-4 : bond 0.00534 ( 7) link_BETA1-4 : angle 2.88666 ( 21) link_BETA1-6 : bond 0.01045 ( 1) link_BETA1-6 : angle 2.85781 ( 3) link_NAG-ASN : bond 0.00685 ( 11) link_NAG-ASN : angle 2.79505 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 248 time to evaluate : 0.403 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: 0.8809 (mtt180) cc_final: 0.8354 (mtm110) REVERT: A 41 TYR cc_start: 0.9320 (m-80) cc_final: 0.8784 (m-80) REVERT: A 65 SER cc_start: 0.9075 (t) cc_final: 0.8735 (p) REVERT: A 69 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8688 (t0) REVERT: A 82 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8739 (mp) REVERT: A 95 MET cc_start: 0.7903 (mtp) cc_final: 0.7371 (mtp) REVERT: A 104 THR cc_start: 0.9040 (m) cc_final: 0.8755 (p) REVERT: A 111 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8579 (tt) REVERT: A 156 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7420 (m-80) REVERT: A 167 LEU cc_start: 0.9301 (tp) cc_final: 0.8980 (tt) REVERT: A 186 GLU cc_start: 0.8040 (tp30) cc_final: 0.7807 (tp30) REVERT: A 204 ASN cc_start: 0.8049 (m-40) cc_final: 0.7044 (t0) REVERT: A 210 PHE cc_start: 0.8521 (t80) cc_final: 0.8282 (t80) REVERT: A 248 CYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6589 (m) REVERT: A 347 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.7965 (mtm) REVERT: A 367 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8344 (mm-40) REVERT: A 428 GLN cc_start: 0.8369 (mt0) cc_final: 0.8120 (mt0) REVERT: A 431 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8615 (mp) REVERT: A 464 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8171 (t0) REVERT: A 472 SER cc_start: 0.5842 (OUTLIER) cc_final: 0.5625 (m) REVERT: A 587 GLN cc_start: 0.7708 (tp40) cc_final: 0.7225 (pt0) REVERT: A 646 SER cc_start: 0.9096 (p) cc_final: 0.8662 (t) REVERT: A 656 ILE cc_start: 0.8710 (pp) cc_final: 0.8499 (pp) REVERT: A 688 TYR cc_start: 0.8218 (t80) cc_final: 0.7949 (t80) REVERT: A 693 LYS cc_start: 0.8653 (mmtp) cc_final: 0.8270 (mtpp) REVERT: B 81 HIS cc_start: 0.8270 (t-90) cc_final: 0.7813 (m90) REVERT: B 86 PHE cc_start: 0.8221 (m-10) cc_final: 0.8006 (m-10) REVERT: B 233 MET cc_start: 0.8533 (tpt) cc_final: 0.8173 (tpt) REVERT: B 421 THR cc_start: 0.9055 (m) cc_final: 0.8704 (p) REVERT: B 429 LYS cc_start: 0.5929 (OUTLIER) cc_final: 0.4929 (mmtt) REVERT: B 432 LEU cc_start: 0.5050 (OUTLIER) cc_final: 0.4613 (tt) REVERT: B 437 ILE cc_start: 0.8327 (tt) cc_final: 0.7790 (mt) REVERT: B 446 TYR cc_start: 0.8323 (t80) cc_final: 0.8115 (t80) REVERT: C 56 LEU cc_start: 0.8541 (mm) cc_final: 0.8320 (tp) REVERT: C 96 LYS cc_start: 0.7251 (mttt) cc_final: 0.7042 (tptt) REVERT: C 109 ARG cc_start: 0.7620 (tpm-80) cc_final: 0.7159 (mtm110) REVERT: C 117 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8033 (ttm) REVERT: C 123 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8577 (tp) REVERT: C 180 ASP cc_start: 0.8316 (t70) cc_final: 0.8077 (t70) REVERT: C 184 ARG cc_start: 0.8421 (mmm-85) cc_final: 0.7997 (mtt180) REVERT: C 218 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7879 (m-80) outliers start: 98 outliers final: 40 residues processed: 310 average time/residue: 0.0980 time to fit residues: 43.7796 Evaluate side-chains 262 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 207 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 367 GLN 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 76 THR Chi-restraints excluded: chain D residue 94 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 114 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN C 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.127904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104269 restraints weight = 15644.185| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.34 r_work: 0.3042 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10280 Z= 0.205 Angle : 0.781 9.260 14036 Z= 0.377 Chirality : 0.048 0.329 1657 Planarity : 0.005 0.047 1705 Dihedral : 12.615 97.855 1861 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.95 % Favored : 94.63 % Rotamer: Outliers : 7.82 % Allowed : 20.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.25), residues: 1211 helix: 2.11 (0.20), residues: 681 sheet: -1.45 (0.44), residues: 122 loop : -2.09 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 84 TYR 0.020 0.002 TYR B 225 PHE 0.045 0.002 PHE B 465 TRP 0.016 0.002 TRP A 257 HIS 0.007 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00477 (10255) covalent geometry : angle 0.76284 (13966) SS BOND : bond 0.00799 ( 5) SS BOND : angle 1.71356 ( 10) hydrogen bonds : bond 0.04416 ( 580) hydrogen bonds : angle 4.82684 ( 1698) link_BETA1-3 : bond 0.00941 ( 1) link_BETA1-3 : angle 1.23583 ( 3) link_BETA1-4 : bond 0.00348 ( 7) link_BETA1-4 : angle 2.51063 ( 21) link_BETA1-6 : bond 0.01051 ( 1) link_BETA1-6 : angle 2.88272 ( 3) link_NAG-ASN : bond 0.00609 ( 11) link_NAG-ASN : angle 2.68859 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 222 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9342 (m-80) cc_final: 0.8944 (m-80) REVERT: A 65 SER cc_start: 0.8881 (t) cc_final: 0.8518 (p) REVERT: A 82 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8784 (mp) REVERT: A 95 MET cc_start: 0.8030 (mtp) cc_final: 0.7751 (ttm) REVERT: A 104 THR cc_start: 0.9023 (m) cc_final: 0.8628 (p) REVERT: A 156 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: A 167 LEU cc_start: 0.9286 (tp) cc_final: 0.8955 (tt) REVERT: A 204 ASN cc_start: 0.7970 (m-40) cc_final: 0.7125 (t0) REVERT: A 248 CYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6563 (m) REVERT: A 347 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7987 (mmm) REVERT: A 464 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8355 (t0) REVERT: A 587 GLN cc_start: 0.7681 (tp40) cc_final: 0.7156 (pt0) REVERT: A 688 TYR cc_start: 0.8274 (t80) cc_final: 0.8018 (t80) REVERT: A 693 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8287 (mtpp) REVERT: A 695 ASP cc_start: 0.7597 (m-30) cc_final: 0.6621 (t70) REVERT: B 81 HIS cc_start: 0.8195 (t-90) cc_final: 0.7868 (m90) REVERT: B 228 MET cc_start: 0.7882 (mtp) cc_final: 0.7671 (mtp) REVERT: B 233 MET cc_start: 0.8705 (tpt) cc_final: 0.8451 (tpt) REVERT: B 245 THR cc_start: 0.7475 (m) cc_final: 0.7105 (p) REVERT: B 429 LYS cc_start: 0.6163 (OUTLIER) cc_final: 0.4847 (mmtt) REVERT: C 96 LYS cc_start: 0.7294 (mttt) cc_final: 0.7011 (tptt) REVERT: C 117 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8050 (mtm) REVERT: C 123 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8647 (tp) REVERT: C 180 ASP cc_start: 0.8353 (t70) cc_final: 0.8114 (t70) REVERT: C 184 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8184 (mtm-85) REVERT: C 218 TYR cc_start: 0.8237 (OUTLIER) cc_final: 0.7896 (m-80) outliers start: 82 outliers final: 44 residues processed: 274 average time/residue: 0.0967 time to fit residues: 38.3089 Evaluate side-chains 257 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 204 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 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 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 356 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 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 665 SER Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 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 390 SER 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 444 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 67 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 42 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.3562 ------------------------------------------------------------------------------- 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 ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103137 restraints weight = 15798.996| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.45 r_work: 0.3083 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10280 Z= 0.176 Angle : 0.726 10.448 14036 Z= 0.352 Chirality : 0.047 0.415 1657 Planarity : 0.005 0.045 1705 Dihedral : 11.414 91.080 1846 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.04 % Favored : 94.55 % Rotamer: Outliers : 6.77 % Allowed : 21.85 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.24), residues: 1211 helix: 1.86 (0.19), residues: 681 sheet: -1.64 (0.43), residues: 120 loop : -2.07 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 84 TYR 0.018 0.002 TYR B 225 PHE 0.045 0.002 PHE B 465 TRP 0.013 0.001 TRP A 257 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00407 (10255) covalent geometry : angle 0.70793 (13966) SS BOND : bond 0.00574 ( 5) SS BOND : angle 1.32647 ( 10) hydrogen bonds : bond 0.04099 ( 580) hydrogen bonds : angle 4.70695 ( 1698) link_BETA1-3 : bond 0.00887 ( 1) link_BETA1-3 : angle 1.20460 ( 3) link_BETA1-4 : bond 0.00347 ( 7) link_BETA1-4 : angle 2.36623 ( 21) link_BETA1-6 : bond 0.01403 ( 1) link_BETA1-6 : angle 3.12933 ( 3) link_NAG-ASN : bond 0.00615 ( 11) link_NAG-ASN : angle 2.66126 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 233 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9337 (m-80) cc_final: 0.9044 (m-80) REVERT: A 65 SER cc_start: 0.8790 (t) cc_final: 0.8478 (p) REVERT: A 95 MET cc_start: 0.8087 (mtp) cc_final: 0.7619 (ttm) REVERT: A 104 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8657 (p) REVERT: A 167 LEU cc_start: 0.9260 (tp) cc_final: 0.8914 (tt) REVERT: A 347 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7864 (mmm) REVERT: A 355 GLN cc_start: 0.8312 (tp40) cc_final: 0.7668 (mm-40) REVERT: A 357 GLU cc_start: 0.8324 (tt0) cc_final: 0.8117 (tt0) REVERT: A 507 PHE cc_start: 0.8209 (m-80) cc_final: 0.7902 (m-80) REVERT: A 587 GLN cc_start: 0.8115 (tp40) cc_final: 0.7665 (pt0) REVERT: A 677 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7020 (t80) REVERT: A 688 TYR cc_start: 0.8320 (t80) cc_final: 0.8088 (t80) REVERT: A 693 LYS cc_start: 0.8641 (mmtp) cc_final: 0.8284 (mtpp) REVERT: A 695 ASP cc_start: 0.7477 (m-30) cc_final: 0.6608 (t70) REVERT: B 228 MET cc_start: 0.7884 (mtp) cc_final: 0.7618 (mtp) REVERT: B 233 MET cc_start: 0.8793 (tpt) cc_final: 0.8493 (tpt) REVERT: B 245 THR cc_start: 0.7724 (m) cc_final: 0.7340 (p) REVERT: B 387 ILE cc_start: 0.9210 (mt) cc_final: 0.8966 (mp) REVERT: B 419 CYS cc_start: 0.8210 (m) cc_final: 0.7520 (t) REVERT: B 421 THR cc_start: 0.9078 (m) cc_final: 0.8738 (p) REVERT: B 429 LYS cc_start: 0.5972 (OUTLIER) cc_final: 0.4745 (mmtt) REVERT: B 446 TYR cc_start: 0.8470 (t80) cc_final: 0.8173 (t80) REVERT: B 450 ASP cc_start: 0.8103 (t0) cc_final: 0.7720 (t0) REVERT: C 96 LYS cc_start: 0.7297 (mttt) cc_final: 0.6976 (tptt) REVERT: C 109 ARG cc_start: 0.7645 (ttp-170) cc_final: 0.7249 (mtm110) REVERT: C 117 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8285 (mtm) REVERT: C 119 TYR cc_start: 0.8576 (t80) cc_final: 0.8319 (t80) REVERT: C 123 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8826 (tp) REVERT: C 180 ASP cc_start: 0.8346 (t70) cc_final: 0.8087 (t70) outliers start: 71 outliers final: 42 residues processed: 282 average time/residue: 0.0897 time to fit residues: 37.1463 Evaluate side-chains 263 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 217 LEU 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 351 LYS 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 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 654 LYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 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 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 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 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 70 VAL 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 25 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 478 ASN A 516 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103139 restraints weight = 15707.806| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.48 r_work: 0.3002 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 10280 Z= 0.284 Angle : 0.790 10.111 14036 Z= 0.386 Chirality : 0.049 0.305 1657 Planarity : 0.005 0.046 1705 Dihedral : 10.547 80.609 1834 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.03 % Favored : 93.64 % Rotamer: Outliers : 7.82 % Allowed : 21.66 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.24), residues: 1211 helix: 1.47 (0.19), residues: 680 sheet: -1.58 (0.42), residues: 119 loop : -2.19 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 105 TYR 0.026 0.002 TYR B 225 PHE 0.043 0.003 PHE B 465 TRP 0.015 0.002 TRP A 653 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00657 (10255) covalent geometry : angle 0.77071 (13966) SS BOND : bond 0.00477 ( 5) SS BOND : angle 1.20036 ( 10) hydrogen bonds : bond 0.04473 ( 580) hydrogen bonds : angle 4.85474 ( 1698) link_BETA1-3 : bond 0.00796 ( 1) link_BETA1-3 : angle 1.96231 ( 3) link_BETA1-4 : bond 0.00273 ( 7) link_BETA1-4 : angle 2.30503 ( 21) link_BETA1-6 : bond 0.01768 ( 1) link_BETA1-6 : angle 3.55313 ( 3) link_NAG-ASN : bond 0.00917 ( 11) link_NAG-ASN : angle 2.96231 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 217 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8234 (mtp) cc_final: 0.7805 (ttm) REVERT: A 156 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.7637 (m-80) REVERT: A 167 LEU cc_start: 0.9287 (tp) cc_final: 0.9027 (tt) REVERT: A 355 GLN cc_start: 0.8392 (tp40) cc_final: 0.7949 (mm-40) REVERT: A 357 GLU cc_start: 0.8302 (tt0) cc_final: 0.8060 (tt0) REVERT: A 522 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8879 (mp) REVERT: A 587 GLN cc_start: 0.8267 (tp40) cc_final: 0.7726 (pt0) REVERT: A 695 ASP cc_start: 0.7417 (m-30) cc_final: 0.6562 (t70) REVERT: B 81 HIS cc_start: 0.8014 (t-90) cc_final: 0.7652 (m90) REVERT: B 225 TYR cc_start: 0.8606 (m-80) cc_final: 0.7719 (m-80) REVERT: B 239 LYS cc_start: 0.8918 (tptt) cc_final: 0.8574 (tttp) REVERT: B 244 TRP cc_start: 0.7015 (OUTLIER) cc_final: 0.5666 (m-90) REVERT: B 245 THR cc_start: 0.7850 (m) cc_final: 0.7623 (p) REVERT: B 387 ILE cc_start: 0.9185 (mt) cc_final: 0.8979 (mp) REVERT: B 421 THR cc_start: 0.9307 (m) cc_final: 0.8978 (p) REVERT: B 429 LYS cc_start: 0.6074 (OUTLIER) cc_final: 0.4721 (mmtt) REVERT: B 446 TYR cc_start: 0.8564 (t80) cc_final: 0.8258 (t80) REVERT: B 450 ASP cc_start: 0.8042 (t0) cc_final: 0.7676 (t0) REVERT: B 459 GLN cc_start: 0.8330 (mt0) cc_final: 0.8113 (mt0) REVERT: C 42 TRP cc_start: 0.9090 (t60) cc_final: 0.8718 (t60) REVERT: C 96 LYS cc_start: 0.7499 (mttt) cc_final: 0.7132 (tptt) REVERT: C 109 ARG cc_start: 0.7587 (ttp-170) cc_final: 0.7186 (mtm110) REVERT: C 117 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8248 (mtm) REVERT: C 119 TYR cc_start: 0.8694 (t80) cc_final: 0.8381 (t80) REVERT: C 123 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8773 (tp) REVERT: C 180 ASP cc_start: 0.8429 (t70) cc_final: 0.7938 (t70) outliers start: 82 outliers final: 54 residues processed: 270 average time/residue: 0.0910 time to fit residues: 36.1828 Evaluate side-chains 267 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 207 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 297 SER 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 509 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 LEU 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 82 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 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 429 LYS Chi-restraints excluded: chain B residue 444 VAL 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 56 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 TRP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.0030 chunk 96 optimal weight: 0.1980 chunk 58 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 A 478 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107483 restraints weight = 15618.751| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.52 r_work: 0.3130 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10280 Z= 0.138 Angle : 0.716 12.025 14036 Z= 0.341 Chirality : 0.047 0.442 1657 Planarity : 0.004 0.040 1705 Dihedral : 9.804 70.618 1829 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.95 % Favored : 94.80 % Rotamer: Outliers : 5.44 % Allowed : 25.86 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.24), residues: 1211 helix: 1.60 (0.19), residues: 680 sheet: -1.55 (0.44), residues: 120 loop : -2.12 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 5 TYR 0.022 0.002 TYR D 47 PHE 0.045 0.002 PHE B 465 TRP 0.014 0.001 TRP A 653 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00301 (10255) covalent geometry : angle 0.69274 (13966) SS BOND : bond 0.00822 ( 5) SS BOND : angle 0.57761 ( 10) hydrogen bonds : bond 0.03817 ( 580) hydrogen bonds : angle 4.59763 ( 1698) link_BETA1-3 : bond 0.00926 ( 1) link_BETA1-3 : angle 1.34101 ( 3) link_BETA1-4 : bond 0.00452 ( 7) link_BETA1-4 : angle 2.09429 ( 21) link_BETA1-6 : bond 0.01567 ( 1) link_BETA1-6 : angle 4.08196 ( 3) link_NAG-ASN : bond 0.00756 ( 11) link_NAG-ASN : angle 3.21443 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 234 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8009 (mtp) cc_final: 0.7652 (ttm) REVERT: A 156 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: A 167 LEU cc_start: 0.9202 (tp) cc_final: 0.8922 (tt) REVERT: A 174 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: A 355 GLN cc_start: 0.8345 (tp40) cc_final: 0.7900 (mm-40) REVERT: A 357 GLU cc_start: 0.8266 (tt0) cc_final: 0.7991 (tt0) REVERT: A 559 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7939 (m) REVERT: A 587 GLN cc_start: 0.8231 (tp40) cc_final: 0.7724 (pt0) REVERT: A 662 LEU cc_start: 0.8978 (mp) cc_final: 0.8736 (mp) REVERT: A 677 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7066 (t80) REVERT: A 695 ASP cc_start: 0.7543 (m-30) cc_final: 0.6804 (t70) REVERT: B 225 TYR cc_start: 0.8477 (m-80) cc_final: 0.7671 (m-80) REVERT: B 244 TRP cc_start: 0.7085 (OUTLIER) cc_final: 0.5986 (m-90) REVERT: B 381 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7654 (tm) REVERT: B 421 THR cc_start: 0.9205 (m) cc_final: 0.8696 (p) REVERT: B 429 LYS cc_start: 0.5956 (OUTLIER) cc_final: 0.4628 (mmtt) REVERT: B 440 THR cc_start: 0.8580 (m) cc_final: 0.8265 (p) REVERT: B 450 ASP cc_start: 0.7979 (t0) cc_final: 0.7540 (t0) REVERT: B 459 GLN cc_start: 0.8102 (mt0) cc_final: 0.7879 (mt0) REVERT: C 42 TRP cc_start: 0.9154 (t60) cc_final: 0.8920 (t60) REVERT: C 112 ILE cc_start: 0.8169 (tt) cc_final: 0.7897 (tp) REVERT: C 117 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8157 (mtm) REVERT: C 119 TYR cc_start: 0.8607 (t80) cc_final: 0.8246 (t80) REVERT: C 123 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8813 (tp) REVERT: C 174 TRP cc_start: 0.8833 (m-10) cc_final: 0.8352 (m-10) REVERT: C 180 ASP cc_start: 0.8282 (t70) cc_final: 0.7989 (t70) outliers start: 57 outliers final: 34 residues processed: 270 average time/residue: 0.0850 time to fit residues: 34.3882 Evaluate side-chains 254 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 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 555 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 654 LYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 168 ILE 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 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 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 117 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 94 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 53 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 0.0170 chunk 59 optimal weight: 4.9990 chunk 108 optimal weight: 0.0370 chunk 32 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.132905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108651 restraints weight = 15530.206| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.48 r_work: 0.3113 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 10280 Z= 0.160 Angle : 0.706 9.783 14036 Z= 0.339 Chirality : 0.046 0.348 1657 Planarity : 0.004 0.044 1705 Dihedral : 9.287 69.585 1829 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.70 % Favored : 94.05 % Rotamer: Outliers : 5.82 % Allowed : 27.00 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.24), residues: 1211 helix: 1.56 (0.19), residues: 679 sheet: -1.24 (0.45), residues: 118 loop : -2.04 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 84 TYR 0.020 0.002 TYR D 47 PHE 0.048 0.002 PHE B 465 TRP 0.010 0.001 TRP A 653 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00375 (10255) covalent geometry : angle 0.68554 (13966) SS BOND : bond 0.00622 ( 5) SS BOND : angle 0.75361 ( 10) hydrogen bonds : bond 0.03903 ( 580) hydrogen bonds : angle 4.62679 ( 1698) link_BETA1-3 : bond 0.00779 ( 1) link_BETA1-3 : angle 1.71403 ( 3) link_BETA1-4 : bond 0.00379 ( 7) link_BETA1-4 : angle 2.13508 ( 21) link_BETA1-6 : bond 0.01349 ( 1) link_BETA1-6 : angle 3.46909 ( 3) link_NAG-ASN : bond 0.00682 ( 11) link_NAG-ASN : angle 2.95333 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 226 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7998 (mtp) cc_final: 0.7558 (ttm) REVERT: A 156 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: A 167 LEU cc_start: 0.9207 (tp) cc_final: 0.8964 (tt) REVERT: A 174 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: A 355 GLN cc_start: 0.8380 (tp40) cc_final: 0.7949 (mm-40) REVERT: A 357 GLU cc_start: 0.8229 (tt0) cc_final: 0.7946 (tt0) REVERT: A 559 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.7926 (m) REVERT: A 662 LEU cc_start: 0.9082 (mp) cc_final: 0.8849 (mp) REVERT: A 677 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7056 (t80) REVERT: A 695 ASP cc_start: 0.7563 (m-30) cc_final: 0.6836 (t70) REVERT: B 225 TYR cc_start: 0.8547 (m-80) cc_final: 0.7735 (m-80) REVERT: B 237 PHE cc_start: 0.8310 (m-80) cc_final: 0.7892 (m-80) REVERT: B 244 TRP cc_start: 0.6985 (OUTLIER) cc_final: 0.5635 (m-90) REVERT: B 381 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7783 (tm) REVERT: B 421 THR cc_start: 0.9078 (m) cc_final: 0.8597 (p) REVERT: B 429 LYS cc_start: 0.5911 (OUTLIER) cc_final: 0.4579 (mmtm) REVERT: B 432 LEU cc_start: 0.5007 (OUTLIER) cc_final: 0.4675 (tt) REVERT: B 440 THR cc_start: 0.8662 (m) cc_final: 0.8385 (p) REVERT: B 446 TYR cc_start: 0.8521 (t80) cc_final: 0.8267 (t80) REVERT: B 450 ASP cc_start: 0.8025 (t0) cc_final: 0.7663 (t0) REVERT: B 459 GLN cc_start: 0.8101 (mt0) cc_final: 0.7879 (mt0) REVERT: C 42 TRP cc_start: 0.9091 (t60) cc_final: 0.8668 (t60) REVERT: C 117 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8147 (mtm) REVERT: C 119 TYR cc_start: 0.8586 (t80) cc_final: 0.8288 (t80) REVERT: C 123 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8857 (tp) REVERT: C 170 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8728 (tp) REVERT: C 174 TRP cc_start: 0.8830 (m-10) cc_final: 0.8311 (m-10) REVERT: C 180 ASP cc_start: 0.8195 (t70) cc_final: 0.7887 (t70) outliers start: 61 outliers final: 37 residues processed: 264 average time/residue: 0.0798 time to fit residues: 31.8118 Evaluate side-chains 257 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 297 SER 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 555 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 654 LYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain 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 117 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 38 optimal weight: 0.0270 chunk 5 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 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 = 0.3595 r_free = 0.3595 target = 0.135165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.111331 restraints weight = 15549.071| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.48 r_work: 0.3131 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 10280 Z= 0.142 Angle : 0.708 10.680 14036 Z= 0.340 Chirality : 0.046 0.503 1657 Planarity : 0.004 0.040 1705 Dihedral : 9.178 69.094 1829 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.78 % Favored : 93.97 % Rotamer: Outliers : 6.11 % Allowed : 26.72 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.24), residues: 1211 helix: 1.48 (0.19), residues: 679 sheet: -1.28 (0.45), residues: 122 loop : -1.93 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 84 TYR 0.016 0.001 TYR C 156 PHE 0.046 0.002 PHE B 465 TRP 0.010 0.001 TRP A 653 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00320 (10255) covalent geometry : angle 0.68864 (13966) SS BOND : bond 0.00440 ( 5) SS BOND : angle 0.57868 ( 10) hydrogen bonds : bond 0.03854 ( 580) hydrogen bonds : angle 4.49939 ( 1698) link_BETA1-3 : bond 0.00755 ( 1) link_BETA1-3 : angle 1.50542 ( 3) link_BETA1-4 : bond 0.00426 ( 7) link_BETA1-4 : angle 2.07289 ( 21) link_BETA1-6 : bond 0.00954 ( 1) link_BETA1-6 : angle 2.80617 ( 3) link_NAG-ASN : bond 0.00981 ( 11) link_NAG-ASN : angle 2.95295 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 226 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7964 (mtp) cc_final: 0.7599 (ttm) REVERT: A 156 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: A 167 LEU cc_start: 0.9171 (tp) cc_final: 0.8940 (tt) REVERT: A 355 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7909 (mm-40) REVERT: A 357 GLU cc_start: 0.8245 (tt0) cc_final: 0.8024 (tt0) REVERT: A 527 ILE cc_start: 0.9014 (mm) cc_final: 0.8808 (mm) REVERT: A 587 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7594 (mm-40) REVERT: A 662 LEU cc_start: 0.9037 (mp) cc_final: 0.8794 (mp) REVERT: A 677 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.7000 (t80) REVERT: A 695 ASP cc_start: 0.7523 (m-30) cc_final: 0.6841 (t70) REVERT: B 225 TYR cc_start: 0.8611 (m-80) cc_final: 0.7822 (m-80) REVERT: B 233 MET cc_start: 0.8779 (tpt) cc_final: 0.8244 (tpt) REVERT: B 237 PHE cc_start: 0.8249 (m-80) cc_final: 0.7746 (m-80) REVERT: B 244 TRP cc_start: 0.6904 (OUTLIER) cc_final: 0.5517 (m-90) REVERT: B 381 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7722 (tm) REVERT: B 421 THR cc_start: 0.9172 (m) cc_final: 0.8707 (p) REVERT: B 429 LYS cc_start: 0.5780 (OUTLIER) cc_final: 0.4537 (mmtm) REVERT: B 432 LEU cc_start: 0.5177 (OUTLIER) cc_final: 0.4920 (tt) REVERT: B 440 THR cc_start: 0.8605 (m) cc_final: 0.8372 (p) REVERT: B 446 TYR cc_start: 0.8526 (t80) cc_final: 0.8217 (t80) REVERT: B 450 ASP cc_start: 0.7978 (t0) cc_final: 0.7639 (t0) REVERT: B 459 GLN cc_start: 0.7998 (mt0) cc_final: 0.7761 (mt0) REVERT: C 42 TRP cc_start: 0.9100 (t60) cc_final: 0.8808 (t60) REVERT: C 48 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8622 (mm) REVERT: C 117 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8137 (mtm) REVERT: C 123 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8780 (tp) REVERT: C 180 ASP cc_start: 0.8263 (t70) cc_final: 0.7894 (t70) outliers start: 64 outliers final: 42 residues processed: 264 average time/residue: 0.0802 time to fit residues: 31.9059 Evaluate side-chains 266 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 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 297 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 555 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 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 432 LEU 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 117 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110735 restraints weight = 15503.177| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.48 r_work: 0.3113 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10280 Z= 0.148 Angle : 0.703 9.443 14036 Z= 0.339 Chirality : 0.046 0.412 1657 Planarity : 0.004 0.043 1705 Dihedral : 9.012 68.140 1826 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.86 % Favored : 93.89 % Rotamer: Outliers : 5.92 % Allowed : 27.10 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.24), residues: 1211 helix: 1.48 (0.19), residues: 680 sheet: -1.22 (0.45), residues: 122 loop : -1.89 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 84 TYR 0.018 0.001 TYR C 156 PHE 0.051 0.002 PHE B 465 TRP 0.015 0.001 TRP D 85 HIS 0.004 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00340 (10255) covalent geometry : angle 0.68387 (13966) SS BOND : bond 0.00470 ( 5) SS BOND : angle 0.52351 ( 10) hydrogen bonds : bond 0.03774 ( 580) hydrogen bonds : angle 4.50379 ( 1698) link_BETA1-3 : bond 0.01005 ( 1) link_BETA1-3 : angle 1.73433 ( 3) link_BETA1-4 : bond 0.00405 ( 7) link_BETA1-4 : angle 2.08597 ( 21) link_BETA1-6 : bond 0.00826 ( 1) link_BETA1-6 : angle 2.40073 ( 3) link_NAG-ASN : bond 0.00887 ( 11) link_NAG-ASN : angle 2.96757 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 214 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7887 (mtp) cc_final: 0.7450 (ttm) REVERT: A 156 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: A 167 LEU cc_start: 0.9174 (tp) cc_final: 0.8955 (tt) REVERT: A 355 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7995 (mm-40) REVERT: A 522 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8926 (mp) REVERT: A 527 ILE cc_start: 0.9021 (mm) cc_final: 0.8800 (mm) REVERT: A 559 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.8084 (t) REVERT: A 587 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7619 (mm-40) REVERT: A 662 LEU cc_start: 0.9056 (mp) cc_final: 0.8803 (mp) REVERT: A 677 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.7036 (t80) REVERT: A 695 ASP cc_start: 0.7491 (m-30) cc_final: 0.6827 (t70) REVERT: B 225 TYR cc_start: 0.8593 (m-80) cc_final: 0.7862 (m-80) REVERT: B 233 MET cc_start: 0.8723 (tpt) cc_final: 0.8140 (tpt) REVERT: B 237 PHE cc_start: 0.8212 (m-80) cc_final: 0.7697 (m-80) REVERT: B 244 TRP cc_start: 0.6907 (OUTLIER) cc_final: 0.5505 (m-90) REVERT: B 381 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7732 (tm) REVERT: B 421 THR cc_start: 0.9111 (m) cc_final: 0.8640 (p) REVERT: B 429 LYS cc_start: 0.5660 (OUTLIER) cc_final: 0.4411 (mmtm) REVERT: B 432 LEU cc_start: 0.5220 (OUTLIER) cc_final: 0.4972 (tt) REVERT: B 440 THR cc_start: 0.8614 (m) cc_final: 0.8376 (p) REVERT: B 446 TYR cc_start: 0.8509 (t80) cc_final: 0.8231 (t80) REVERT: B 450 ASP cc_start: 0.7969 (t0) cc_final: 0.7625 (t0) REVERT: B 459 GLN cc_start: 0.8019 (mt0) cc_final: 0.7751 (mt0) REVERT: C 42 TRP cc_start: 0.9100 (t60) cc_final: 0.8687 (t60) REVERT: C 48 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8633 (mm) REVERT: C 117 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8109 (mtm) REVERT: C 123 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8781 (tp) REVERT: C 180 ASP cc_start: 0.8266 (t70) cc_final: 0.7895 (t70) outliers start: 62 outliers final: 39 residues processed: 251 average time/residue: 0.0760 time to fit residues: 29.0666 Evaluate side-chains 261 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 210 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 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 297 SER Chi-restraints excluded: chain A residue 355 GLN 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 436 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 432 LEU 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 117 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 51 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 0.0050 chunk 30 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111980 restraints weight = 15447.074| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.46 r_work: 0.3100 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10280 Z= 0.142 Angle : 0.701 10.551 14036 Z= 0.337 Chirality : 0.046 0.434 1657 Planarity : 0.004 0.041 1705 Dihedral : 8.899 67.601 1826 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.11 % Favored : 93.72 % Rotamer: Outliers : 5.25 % Allowed : 28.24 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.24), residues: 1211 helix: 1.51 (0.19), residues: 681 sheet: -1.16 (0.45), residues: 122 loop : -1.86 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 84 TYR 0.017 0.001 TYR B 225 PHE 0.053 0.002 PHE B 465 TRP 0.014 0.001 TRP D 85 HIS 0.005 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00327 (10255) covalent geometry : angle 0.68054 (13966) SS BOND : bond 0.00440 ( 5) SS BOND : angle 0.50042 ( 10) hydrogen bonds : bond 0.03722 ( 580) hydrogen bonds : angle 4.47976 ( 1698) link_BETA1-3 : bond 0.00746 ( 1) link_BETA1-3 : angle 1.45511 ( 3) link_BETA1-4 : bond 0.00393 ( 7) link_BETA1-4 : angle 2.03360 ( 21) link_BETA1-6 : bond 0.00791 ( 1) link_BETA1-6 : angle 2.11992 ( 3) link_NAG-ASN : bond 0.00822 ( 11) link_NAG-ASN : angle 3.06885 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7853 (mtp) cc_final: 0.7433 (ttm) REVERT: A 108 MET cc_start: 0.8400 (tpp) cc_final: 0.8082 (mmm) REVERT: A 156 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.7531 (m-80) REVERT: A 167 LEU cc_start: 0.9164 (tp) cc_final: 0.8942 (tt) REVERT: A 559 SER cc_start: 0.8275 (OUTLIER) cc_final: 0.8049 (t) REVERT: A 587 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7632 (mm-40) REVERT: A 662 LEU cc_start: 0.9041 (mp) cc_final: 0.8768 (mp) REVERT: A 677 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.7045 (t80) REVERT: A 695 ASP cc_start: 0.7495 (m-30) cc_final: 0.6827 (t70) REVERT: B 93 MET cc_start: 0.8058 (ptt) cc_final: 0.7758 (ptt) REVERT: B 225 TYR cc_start: 0.8590 (m-80) cc_final: 0.7861 (m-80) REVERT: B 228 MET cc_start: 0.7758 (mtp) cc_final: 0.7394 (mtp) REVERT: B 233 MET cc_start: 0.8706 (tpt) cc_final: 0.8129 (tpt) REVERT: B 237 PHE cc_start: 0.8203 (m-80) cc_final: 0.7684 (m-80) REVERT: B 244 TRP cc_start: 0.6868 (OUTLIER) cc_final: 0.5483 (m-90) REVERT: B 381 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7659 (tm) REVERT: B 421 THR cc_start: 0.9130 (m) cc_final: 0.8801 (p) REVERT: B 429 LYS cc_start: 0.5563 (OUTLIER) cc_final: 0.4378 (mmtm) REVERT: B 432 LEU cc_start: 0.5205 (OUTLIER) cc_final: 0.4971 (tt) REVERT: B 440 THR cc_start: 0.8581 (m) cc_final: 0.8352 (p) REVERT: B 446 TYR cc_start: 0.8485 (t80) cc_final: 0.8231 (t80) REVERT: B 450 ASP cc_start: 0.7991 (t0) cc_final: 0.7639 (t0) REVERT: B 459 GLN cc_start: 0.8026 (mt0) cc_final: 0.7750 (mt0) REVERT: C 42 TRP cc_start: 0.9112 (t60) cc_final: 0.8694 (t60) REVERT: C 48 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8625 (mm) REVERT: C 117 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8084 (mtm) REVERT: C 123 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8764 (tp) outliers start: 55 outliers final: 39 residues processed: 250 average time/residue: 0.0746 time to fit residues: 28.3031 Evaluate side-chains 261 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 212 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 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 217 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 351 LYS 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 436 ILE Chi-restraints excluded: chain A residue 494 LEU 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 632 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 48 LEU 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 117 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN B 223 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.134759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.110728 restraints weight = 15703.116| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.49 r_work: 0.3084 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10280 Z= 0.157 Angle : 0.702 9.930 14036 Z= 0.339 Chirality : 0.045 0.440 1657 Planarity : 0.004 0.043 1705 Dihedral : 8.787 66.583 1826 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.03 % Favored : 93.81 % Rotamer: Outliers : 5.25 % Allowed : 28.05 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.24), residues: 1211 helix: 1.46 (0.19), residues: 680 sheet: -1.20 (0.45), residues: 122 loop : -1.85 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 84 TYR 0.021 0.001 TYR B 225 PHE 0.052 0.002 PHE B 465 TRP 0.013 0.001 TRP D 85 HIS 0.005 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00365 (10255) covalent geometry : angle 0.68262 (13966) SS BOND : bond 0.00523 ( 5) SS BOND : angle 0.54703 ( 10) hydrogen bonds : bond 0.03753 ( 580) hydrogen bonds : angle 4.49300 ( 1698) link_BETA1-3 : bond 0.00713 ( 1) link_BETA1-3 : angle 1.59398 ( 3) link_BETA1-4 : bond 0.00381 ( 7) link_BETA1-4 : angle 2.01681 ( 21) link_BETA1-6 : bond 0.00729 ( 1) link_BETA1-6 : angle 1.85445 ( 3) link_NAG-ASN : bond 0.00753 ( 11) link_NAG-ASN : angle 3.00151 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2117.26 seconds wall clock time: 37 minutes 14.25 seconds (2234.25 seconds total)