Starting phenix.real_space_refine on Wed Sep 25 13:50:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/09_2024/5a63_3061.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/09_2024/5a63_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/09_2024/5a63_3061.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/09_2024/5a63_3061.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/09_2024/5a63_3061.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/09_2024/5a63_3061.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 35 5.16 5 C 6536 2.51 5 N 1589 2.21 5 O 1841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10003 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5222 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 37, 'TRANS': 627} Chain: "B" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1702 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 6, 'TRANS': 208} Chain breaks: 2 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 850 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 6.02, per 1000 atoms: 0.60 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: 2.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2298 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 6 sheets defined 60.9% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 34 through 40 removed outlier: 3.949A pdb=" N ARG A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.515A pdb=" N LEU A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.558A pdb=" N MET A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.787A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.621A pdb=" N CYS A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 removed outlier: 4.047A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.665A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 434 removed outlier: 4.147A pdb=" N ALA A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 474 through 479 removed outlier: 4.239A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 503 Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.610A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 Processing helix chain 'A' and resid 541 through 546 removed outlier: 3.810A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.756A pdb=" N TYR A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 567 " --> pdb=" O THR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 665 through 693 Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'B' and resid 78 through 104 Proline residue: B 88 - end of helix removed outlier: 3.671A pdb=" N SER B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 108 Processing helix chain 'B' and resid 167 through 190 removed outlier: 4.219A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 241 Processing helix chain 'B' and resid 242 through 260 removed outlier: 3.544A pdb=" N ALA B 251 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 399 Processing helix chain 'B' and resid 404 through 428 Processing helix chain 'B' and resid 435 through 452 Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.288A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 24 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 28 through 61 Processing helix chain 'C' and resid 64 through 103 removed outlier: 3.851A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 142 removed outlier: 3.553A pdb=" N TYR C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 141 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.500A pdb=" N THR C 172 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 206 removed outlier: 3.786A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 232 removed outlier: 4.074A pdb=" N LEU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.651A pdb=" N LEU C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 removed outlier: 3.761A pdb=" N ARG D 5 " --> pdb=" O ASN D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 22 Processing helix chain 'D' and resid 26 through 36 Processing helix chain 'D' and resid 37 through 44 Processing helix chain 'D' and resid 49 through 85 removed outlier: 3.597A pdb=" N TRP D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) Proline residue: D 83 - end of helix Processing helix chain 'D' and resid 86 through 92 removed outlier: 3.813A pdb=" N ASP D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 41 through 44 removed outlier: 4.633A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 13.686A pdb=" N VAL A 75 " --> pdb=" O PRO A 211 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AC, first strand: chain 'A' and resid 175 through 176 Processing sheet with id=AD, first strand: chain 'A' and resid 412 through 414 removed outlier: 7.400A pdb=" N VAL A 277 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE A 362 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA A 279 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A 364 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG A 281 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N GLY A 366 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A 253 " --> pdb=" O ALA A 630 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.091A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.858A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1698 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 3.08 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: 0.240 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.790 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.440 ------------------------------------------------------------------------------- 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 : 0.010 0.131 10255 Z= 0.656 Angle : 1.689 17.252 13966 Z= 1.178 Chirality : 0.109 1.305 1657 Planarity : 0.008 0.106 1705 Dihedral : 20.477 121.149 3951 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 39.51 Ramachandran Plot: Outliers : 2.15 % Allowed : 6.36 % Favored : 91.49 % Rotamer: Outliers : 13.74 % Allowed : 12.12 % Favored : 74.14 % Cbeta Deviations : 0.70 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.22), residues: 1211 helix: 1.34 (0.17), residues: 672 sheet: -1.51 (0.48), residues: 113 loop : -2.13 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 289 HIS 0.007 0.002 HIS A 199 PHE 0.033 0.003 PHE B 386 TYR 0.031 0.003 TYR B 225 ARG 0.009 0.001 ARG A 657 *********************** 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 fitting. rotamer outliers: 144 poor density : 299 time to evaluate : 0.974 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: 0.2354 time to fit residues: 128.9232 Evaluate side-chains 265 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 208 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 429 ARG Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 94 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 163 GLN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN A 367 GLN A 418 GLN A 428 GLN A 449 HIS ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN A 587 GLN A 606 GLN B 464 GLN C 136 ASN C 207 ASN D 79 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4101 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10255 Z= 0.278 Angle : 0.821 11.758 13966 Z= 0.410 Chirality : 0.052 0.370 1657 Planarity : 0.006 0.049 1705 Dihedral : 15.096 104.575 1926 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.87 % Favored : 94.72 % Rotamer: Outliers : 9.26 % Allowed : 17.94 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1211 helix: 2.39 (0.20), residues: 688 sheet: -1.55 (0.44), residues: 118 loop : -2.30 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 257 HIS 0.011 0.002 HIS A 553 PHE 0.040 0.003 PHE B 465 TYR 0.020 0.002 TYR A 569 ARG 0.011 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 250 time to evaluate : 0.991 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: 0.6454 (mtt180) cc_final: 0.6226 (mtm110) REVERT: A 80 GLU cc_start: 0.6566 (mm-30) cc_final: 0.6171 (tt0) REVERT: A 156 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.6040 (m-80) REVERT: A 167 LEU cc_start: 0.6061 (tp) cc_final: 0.5784 (tt) REVERT: A 204 ASN cc_start: 0.7782 (m-40) cc_final: 0.6947 (t0) REVERT: A 210 PHE cc_start: 0.5264 (t80) cc_final: 0.4974 (t80) REVERT: A 213 CYS cc_start: 0.7072 (t) cc_final: 0.6498 (t) REVERT: A 248 CYS cc_start: 0.4241 (OUTLIER) cc_final: 0.3752 (m) REVERT: A 253 ASP cc_start: 0.6929 (p0) cc_final: 0.6661 (p0) REVERT: A 280 THR cc_start: 0.5607 (OUTLIER) cc_final: 0.5139 (p) REVERT: A 283 ASP cc_start: 0.5564 (p0) cc_final: 0.5084 (p0) REVERT: A 367 GLN cc_start: 0.4242 (OUTLIER) cc_final: 0.3955 (mm-40) REVERT: A 431 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6339 (mp) REVERT: A 464 ASN cc_start: 0.5926 (OUTLIER) cc_final: 0.5675 (t0) REVERT: A 516 GLN cc_start: 0.6763 (tt0) cc_final: 0.6520 (tp40) REVERT: A 541 ASP cc_start: 0.7752 (m-30) cc_final: 0.7382 (t0) REVERT: A 587 GLN cc_start: 0.7781 (tp40) cc_final: 0.7219 (pt0) REVERT: A 693 LYS cc_start: 0.6265 (mmtp) cc_final: 0.5972 (mtpp) REVERT: B 446 TYR cc_start: 0.6417 (t80) cc_final: 0.6211 (t80) REVERT: C 96 LYS cc_start: 0.5583 (mttt) cc_final: 0.5247 (tptt) REVERT: C 109 ARG cc_start: 0.6308 (tpm-80) cc_final: 0.6102 (mtm110) REVERT: C 123 LEU cc_start: 0.5741 (OUTLIER) cc_final: 0.5527 (tp) REVERT: D 11 LYS cc_start: 0.4900 (mtpt) cc_final: 0.4668 (mtpt) outliers start: 97 outliers final: 43 residues processed: 312 average time/residue: 0.2031 time to fit residues: 90.9133 Evaluate side-chains 253 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 203 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 112 LYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 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 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 C residue 5 VAL Chi-restraints excluded: chain C residue 113 SER 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 D residue 12 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 TRP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 98 optimal weight: 0.0010 chunk 109 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- 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 428 GLN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN C 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4121 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10255 Z= 0.264 Angle : 0.746 10.026 13966 Z= 0.364 Chirality : 0.047 0.311 1657 Planarity : 0.005 0.048 1705 Dihedral : 12.204 96.396 1853 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.04 % Favored : 94.55 % Rotamer: Outliers : 6.20 % Allowed : 22.61 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1211 helix: 2.07 (0.20), residues: 688 sheet: -1.41 (0.43), residues: 125 loop : -2.11 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 209 HIS 0.007 0.001 HIS A 553 PHE 0.045 0.002 PHE B 465 TYR 0.018 0.002 TYR B 225 ARG 0.007 0.001 ARG D 84 *********************** 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 299 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 234 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6640 (mm-30) cc_final: 0.6248 (tt0) REVERT: A 167 LEU cc_start: 0.6062 (tp) cc_final: 0.5755 (tt) REVERT: A 200 ASN cc_start: 0.2981 (m-40) cc_final: 0.2538 (m110) REVERT: A 204 ASN cc_start: 0.7716 (m-40) cc_final: 0.7008 (t0) REVERT: A 213 CYS cc_start: 0.6813 (t) cc_final: 0.6023 (t) REVERT: A 247 VAL cc_start: 0.4584 (OUTLIER) cc_final: 0.4171 (p) REVERT: A 248 CYS cc_start: 0.4586 (OUTLIER) cc_final: 0.4269 (m) REVERT: A 280 THR cc_start: 0.5528 (m) cc_final: 0.5062 (p) REVERT: A 355 GLN cc_start: 0.5612 (tp40) cc_final: 0.5409 (mm-40) REVERT: A 357 GLU cc_start: 0.7804 (tt0) cc_final: 0.7579 (tt0) REVERT: A 464 ASN cc_start: 0.5960 (OUTLIER) cc_final: 0.5740 (t0) REVERT: A 541 ASP cc_start: 0.7889 (m-30) cc_final: 0.7640 (t0) REVERT: A 587 GLN cc_start: 0.7815 (tp40) cc_final: 0.7218 (pt0) REVERT: A 591 LYS cc_start: 0.8381 (ttpp) cc_final: 0.8084 (mttm) REVERT: A 693 LYS cc_start: 0.6292 (mmtp) cc_final: 0.5998 (mtpp) REVERT: A 695 ASP cc_start: 0.7313 (m-30) cc_final: 0.7035 (t70) REVERT: C 96 LYS cc_start: 0.5455 (mttt) cc_final: 0.5125 (tptt) REVERT: C 109 ARG cc_start: 0.6346 (tpm-80) cc_final: 0.6098 (mtm110) REVERT: C 123 LEU cc_start: 0.5698 (OUTLIER) cc_final: 0.5447 (tp) outliers start: 65 outliers final: 36 residues processed: 275 average time/residue: 0.2119 time to fit residues: 83.3442 Evaluate side-chains 252 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 212 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 174 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 247 VAL 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 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 TRP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 12 optimal weight: 0.1980 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 222 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4128 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10255 Z= 0.287 Angle : 0.707 11.834 13966 Z= 0.349 Chirality : 0.046 0.307 1657 Planarity : 0.005 0.046 1705 Dihedral : 11.036 89.957 1834 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.37 % Favored : 94.22 % Rotamer: Outliers : 6.68 % Allowed : 23.19 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1211 helix: 1.89 (0.19), residues: 681 sheet: -1.67 (0.43), residues: 120 loop : -2.01 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 257 HIS 0.006 0.001 HIS A 553 PHE 0.044 0.002 PHE B 465 TYR 0.020 0.002 TYR B 225 ARG 0.004 0.001 ARG D 84 *********************** 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 291 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 221 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6300 (tt0) REVERT: A 94 TYR cc_start: 0.4674 (OUTLIER) cc_final: 0.4389 (m-80) REVERT: A 156 PHE cc_start: 0.6709 (OUTLIER) cc_final: 0.6311 (m-80) REVERT: A 167 LEU cc_start: 0.6075 (tp) cc_final: 0.5763 (tt) REVERT: A 200 ASN cc_start: 0.3275 (m-40) cc_final: 0.2938 (m-40) REVERT: A 213 CYS cc_start: 0.6867 (t) cc_final: 0.6031 (t) REVERT: A 247 VAL cc_start: 0.4689 (OUTLIER) cc_final: 0.4281 (p) REVERT: A 248 CYS cc_start: 0.4961 (OUTLIER) cc_final: 0.4541 (m) REVERT: A 280 THR cc_start: 0.5042 (m) cc_final: 0.4824 (p) REVERT: A 357 GLU cc_start: 0.7657 (tt0) cc_final: 0.7421 (tt0) REVERT: A 541 ASP cc_start: 0.7896 (m-30) cc_final: 0.7664 (t0) REVERT: A 587 GLN cc_start: 0.7848 (tp40) cc_final: 0.7239 (pt0) REVERT: A 591 LYS cc_start: 0.8606 (ttpp) cc_final: 0.8341 (mttm) REVERT: A 693 LYS cc_start: 0.6612 (mmtp) cc_final: 0.6317 (mtpp) REVERT: A 695 ASP cc_start: 0.7203 (m-30) cc_final: 0.6908 (t70) REVERT: B 244 TRP cc_start: 0.5693 (OUTLIER) cc_final: 0.4322 (m-90) REVERT: C 96 LYS cc_start: 0.5440 (mttt) cc_final: 0.5116 (tptt) REVERT: C 109 ARG cc_start: 0.6390 (tpm-80) cc_final: 0.6135 (mtm110) outliers start: 70 outliers final: 43 residues processed: 267 average time/residue: 0.1918 time to fit residues: 73.9081 Evaluate side-chains 254 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 206 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 312 LEU 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 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 LEU 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 152 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 355 GLN A 462 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4134 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10255 Z= 0.331 Angle : 0.721 11.352 13966 Z= 0.355 Chirality : 0.048 0.402 1657 Planarity : 0.004 0.047 1705 Dihedral : 10.292 80.004 1826 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.78 % Favored : 93.89 % Rotamer: Outliers : 7.25 % Allowed : 23.09 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1211 helix: 1.71 (0.19), residues: 681 sheet: -1.84 (0.41), residues: 120 loop : -2.05 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 653 HIS 0.007 0.001 HIS A 553 PHE 0.042 0.002 PHE B 465 TYR 0.022 0.002 TYR B 225 ARG 0.003 0.001 ARG C 62 *********************** 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 305 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 229 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.6092 (OUTLIER) cc_final: 0.5719 (t0) REVERT: A 80 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6325 (tt0) REVERT: A 156 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.6348 (m-80) REVERT: A 167 LEU cc_start: 0.6347 (tp) cc_final: 0.6033 (tt) REVERT: A 200 ASN cc_start: 0.3244 (m-40) cc_final: 0.2811 (m-40) REVERT: A 213 CYS cc_start: 0.6799 (t) cc_final: 0.5983 (t) REVERT: A 221 MET cc_start: 0.7106 (mmt) cc_final: 0.6728 (mmt) REVERT: A 247 VAL cc_start: 0.4662 (OUTLIER) cc_final: 0.4304 (p) REVERT: A 280 THR cc_start: 0.5304 (m) cc_final: 0.5061 (p) REVERT: A 357 GLU cc_start: 0.7498 (tt0) cc_final: 0.7244 (tt0) REVERT: A 507 PHE cc_start: 0.5898 (m-80) cc_final: 0.5633 (m-80) REVERT: A 541 ASP cc_start: 0.7899 (m-30) cc_final: 0.7683 (t0) REVERT: A 591 LYS cc_start: 0.8671 (ttpp) cc_final: 0.8385 (mttm) REVERT: A 693 LYS cc_start: 0.6609 (mmtp) cc_final: 0.6326 (mtpp) REVERT: A 695 ASP cc_start: 0.6990 (m-30) cc_final: 0.6713 (t70) REVERT: B 225 TYR cc_start: 0.4695 (m-80) cc_final: 0.4489 (m-80) REVERT: B 244 TRP cc_start: 0.5555 (OUTLIER) cc_final: 0.4457 (m-90) REVERT: C 96 LYS cc_start: 0.5518 (mttt) cc_final: 0.5182 (tptt) outliers start: 76 outliers final: 51 residues processed: 277 average time/residue: 0.1868 time to fit residues: 75.2248 Evaluate side-chains 271 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 216 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 86 LEU Chi-restraints excluded: chain A residue 95 MET 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 247 VAL Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 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 C residue 5 VAL 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 124 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 207 ASN 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 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 105 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 199 HIS ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4132 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10255 Z= 0.248 Angle : 0.695 10.797 13966 Z= 0.341 Chirality : 0.046 0.300 1657 Planarity : 0.004 0.046 1705 Dihedral : 9.736 71.522 1823 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.45 % Favored : 94.30 % Rotamer: Outliers : 6.39 % Allowed : 24.71 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.24), residues: 1211 helix: 1.71 (0.19), residues: 680 sheet: -1.68 (0.42), residues: 116 loop : -1.99 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 174 HIS 0.006 0.001 HIS A 553 PHE 0.051 0.002 PHE B 465 TYR 0.017 0.002 TYR C 156 ARG 0.005 0.000 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 223 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6376 (tt0) REVERT: A 156 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.6394 (m-80) REVERT: A 167 LEU cc_start: 0.6160 (tp) cc_final: 0.5828 (tt) REVERT: A 200 ASN cc_start: 0.2943 (m-40) cc_final: 0.2634 (m-40) REVERT: A 213 CYS cc_start: 0.6732 (t) cc_final: 0.5717 (t) REVERT: A 221 MET cc_start: 0.7193 (mmt) cc_final: 0.6867 (mmt) REVERT: A 248 CYS cc_start: 0.4821 (OUTLIER) cc_final: 0.4343 (m) REVERT: A 305 GLN cc_start: 0.6269 (tp40) cc_final: 0.6057 (tp40) REVERT: A 507 PHE cc_start: 0.6123 (m-80) cc_final: 0.5887 (m-80) REVERT: A 695 ASP cc_start: 0.7056 (m-30) cc_final: 0.6810 (t70) REVERT: B 225 TYR cc_start: 0.4682 (m-80) cc_final: 0.4478 (m-80) REVERT: B 244 TRP cc_start: 0.5441 (OUTLIER) cc_final: 0.4368 (m-90) REVERT: C 96 LYS cc_start: 0.5561 (mttt) cc_final: 0.5220 (tptt) outliers start: 67 outliers final: 49 residues processed: 265 average time/residue: 0.1870 time to fit residues: 72.4842 Evaluate side-chains 260 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 208 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 95 MET 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 189 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 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 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 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 124 SER Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 217 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 5.9990 chunk 66 optimal weight: 0.4980 chunk 85 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4134 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10255 Z= 0.224 Angle : 0.691 9.391 13966 Z= 0.340 Chirality : 0.047 0.473 1657 Planarity : 0.004 0.043 1705 Dihedral : 9.296 71.215 1823 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.95 % Favored : 93.81 % Rotamer: Outliers : 6.01 % Allowed : 25.57 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1211 helix: 1.65 (0.19), residues: 678 sheet: -1.46 (0.44), residues: 118 loop : -1.96 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 174 HIS 0.005 0.001 HIS C 150 PHE 0.049 0.002 PHE B 465 TYR 0.019 0.001 TYR C 210 ARG 0.005 0.000 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 238 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6364 (tt0) REVERT: A 156 PHE cc_start: 0.6867 (OUTLIER) cc_final: 0.6419 (m-80) REVERT: A 167 LEU cc_start: 0.6400 (tp) cc_final: 0.6095 (tt) REVERT: A 200 ASN cc_start: 0.2847 (m-40) cc_final: 0.2479 (m-40) REVERT: A 213 CYS cc_start: 0.6697 (t) cc_final: 0.5807 (t) REVERT: A 221 MET cc_start: 0.7265 (mmt) cc_final: 0.7062 (mmt) REVERT: A 247 VAL cc_start: 0.4669 (p) cc_final: 0.4250 (p) REVERT: A 248 CYS cc_start: 0.4622 (OUTLIER) cc_final: 0.4071 (m) REVERT: A 507 PHE cc_start: 0.6144 (m-80) cc_final: 0.5908 (m-80) REVERT: A 559 SER cc_start: 0.5137 (OUTLIER) cc_final: 0.4906 (m) REVERT: A 656 ILE cc_start: 0.5824 (OUTLIER) cc_final: 0.5395 (mt) REVERT: A 695 ASP cc_start: 0.7040 (m-30) cc_final: 0.6800 (t70) REVERT: B 244 TRP cc_start: 0.5414 (OUTLIER) cc_final: 0.4331 (m-90) REVERT: C 96 LYS cc_start: 0.5508 (mttt) cc_final: 0.5157 (tptt) outliers start: 63 outliers final: 45 residues processed: 275 average time/residue: 0.1903 time to fit residues: 76.5747 Evaluate side-chains 268 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 218 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 95 MET 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 248 CYS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 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 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 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 124 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 70 VAL 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 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 111 optimal weight: 0.0670 chunk 101 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS C 207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4138 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 10255 Z= 0.216 Angle : 0.680 9.408 13966 Z= 0.333 Chirality : 0.045 0.349 1657 Planarity : 0.004 0.043 1705 Dihedral : 9.017 70.655 1823 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.95 % Favored : 93.81 % Rotamer: Outliers : 5.92 % Allowed : 27.00 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1211 helix: 1.64 (0.19), residues: 679 sheet: -1.35 (0.45), residues: 118 loop : -1.90 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 174 HIS 0.004 0.001 HIS A 553 PHE 0.053 0.002 PHE B 465 TYR 0.023 0.001 TYR C 156 ARG 0.006 0.000 ARG D 84 *********************** 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 fitting. rotamer outliers: 62 poor density : 228 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6361 (tt0) REVERT: A 156 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6539 (m-80) REVERT: A 167 LEU cc_start: 0.6444 (tp) cc_final: 0.6137 (tt) REVERT: A 248 CYS cc_start: 0.4533 (OUTLIER) cc_final: 0.3925 (m) REVERT: A 507 PHE cc_start: 0.6328 (m-80) cc_final: 0.6124 (m-80) REVERT: A 559 SER cc_start: 0.5434 (OUTLIER) cc_final: 0.5159 (m) REVERT: A 656 ILE cc_start: 0.5819 (OUTLIER) cc_final: 0.5416 (mt) REVERT: A 695 ASP cc_start: 0.7029 (m-30) cc_final: 0.6798 (t70) REVERT: B 244 TRP cc_start: 0.5347 (OUTLIER) cc_final: 0.4277 (m-90) outliers start: 62 outliers final: 46 residues processed: 265 average time/residue: 0.1859 time to fit residues: 72.0872 Evaluate side-chains 264 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 213 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 95 MET 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 189 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 200 LEU 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 390 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 70 VAL 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 111 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4145 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 10255 Z= 0.218 Angle : 0.685 9.431 13966 Z= 0.334 Chirality : 0.046 0.377 1657 Planarity : 0.004 0.044 1705 Dihedral : 8.892 69.958 1820 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.95 % Favored : 93.81 % Rotamer: Outliers : 6.01 % Allowed : 27.10 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1211 helix: 1.61 (0.19), residues: 679 sheet: -1.40 (0.45), residues: 121 loop : -1.89 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP C 174 HIS 0.004 0.001 HIS C 197 PHE 0.047 0.002 PHE B 465 TYR 0.026 0.001 TYR C 156 ARG 0.005 0.000 ARG D 84 *********************** 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 286 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 223 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6360 (tt0) REVERT: A 156 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6544 (m-80) REVERT: A 167 LEU cc_start: 0.6440 (tp) cc_final: 0.6130 (tt) REVERT: A 213 CYS cc_start: 0.6953 (t) cc_final: 0.6352 (t) REVERT: A 248 CYS cc_start: 0.4556 (OUTLIER) cc_final: 0.3957 (m) REVERT: A 559 SER cc_start: 0.5545 (OUTLIER) cc_final: 0.5322 (m) REVERT: A 656 ILE cc_start: 0.5844 (OUTLIER) cc_final: 0.5424 (mt) REVERT: A 695 ASP cc_start: 0.7020 (m-30) cc_final: 0.6789 (t70) REVERT: B 244 TRP cc_start: 0.5161 (OUTLIER) cc_final: 0.4135 (m-90) outliers start: 63 outliers final: 47 residues processed: 259 average time/residue: 0.1856 time to fit residues: 70.5773 Evaluate side-chains 269 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 217 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 189 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 302 PHE Chi-restraints excluded: chain A residue 318 VAL 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 436 ILE 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 656 ILE Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain 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 124 SER Chi-restraints excluded: chain C residue 137 ILE 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 66 PHE 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 88 LEU 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 54 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 120 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4150 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10255 Z= 0.222 Angle : 0.685 9.428 13966 Z= 0.334 Chirality : 0.046 0.435 1657 Planarity : 0.004 0.045 1705 Dihedral : 8.775 69.382 1820 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.86 % Favored : 93.89 % Rotamer: Outliers : 5.53 % Allowed : 27.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1211 helix: 1.56 (0.19), residues: 681 sheet: -1.39 (0.46), residues: 121 loop : -1.87 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 174 HIS 0.005 0.001 HIS C 197 PHE 0.045 0.002 PHE B 465 TYR 0.014 0.001 TYR C 156 ARG 0.005 0.000 ARG D 84 ********************** 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 284 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 226 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6360 (tt0) REVERT: A 156 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6566 (m-80) REVERT: A 167 LEU cc_start: 0.6442 (tp) cc_final: 0.6132 (tt) REVERT: A 213 CYS cc_start: 0.7050 (t) cc_final: 0.6484 (t) REVERT: A 218 PHE cc_start: 0.5192 (m-80) cc_final: 0.4920 (m-80) REVERT: A 248 CYS cc_start: 0.4510 (OUTLIER) cc_final: 0.3917 (m) REVERT: A 656 ILE cc_start: 0.5825 (OUTLIER) cc_final: 0.5412 (mt) REVERT: A 695 ASP cc_start: 0.7011 (m-30) cc_final: 0.6785 (t70) REVERT: B 244 TRP cc_start: 0.5094 (OUTLIER) cc_final: 0.4076 (m-90) outliers start: 58 outliers final: 46 residues processed: 259 average time/residue: 0.1848 time to fit residues: 71.1958 Evaluate side-chains 270 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 220 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 189 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 302 PHE Chi-restraints excluded: chain A residue 318 VAL 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 436 ILE Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 200 LEU 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 390 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE 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 124 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE 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 88 LEU 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 88 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** B 463 HIS ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3593 r_free = 0.3593 target = 0.134917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110874 restraints weight = 15487.398| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.48 r_work: 0.3133 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10255 Z= 0.267 Angle : 0.703 9.490 13966 Z= 0.343 Chirality : 0.046 0.426 1657 Planarity : 0.004 0.045 1705 Dihedral : 8.718 68.313 1820 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.03 % Favored : 93.81 % Rotamer: Outliers : 5.53 % Allowed : 28.24 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1211 helix: 1.47 (0.19), residues: 682 sheet: -1.47 (0.45), residues: 121 loop : -1.83 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 174 HIS 0.006 0.001 HIS B 463 PHE 0.053 0.002 PHE B 465 TYR 0.014 0.002 TYR A 565 ARG 0.005 0.000 ARG D 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2382.51 seconds wall clock time: 42 minutes 59.80 seconds (2579.80 seconds total)