Starting phenix.real_space_refine on Thu Mar 14 22:46:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/03_2024/5a63_3061_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/03_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_3061/03_2024/5a63_3061.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/03_2024/5a63_3061.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/03_2024/5a63_3061_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a63_3061/03_2024/5a63_3061_updated.pdb" } 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 Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.84, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 5.17 Conformation dependent library (CDL) restraints added in 1.9 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... running ksdssp... Secondary structure from input PDB file: 45 helices and 5 sheets defined 54.5% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 79 through 86 Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.579A pdb=" N ARG A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 186 through 199 Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 299 through 314 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 340 through 349 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 388 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 426 through 433 removed outlier: 4.147A pdb=" N ALA A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 463 No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 482 through 502 Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 535 through 537 No H-bonds generated for 'chain 'A' and resid 535 through 537' Processing helix chain 'A' and resid 542 through 545 Processing helix chain 'A' and resid 562 through 575 removed outlier: 3.515A pdb=" N VAL A 567 " --> pdb=" O THR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 633 through 636 No H-bonds generated for 'chain 'A' and resid 633 through 636' Processing helix chain 'A' and resid 666 through 692 Processing helix chain 'A' and resid 694 through 697 No H-bonds generated for 'chain 'A' and resid 694 through 697' Processing helix chain 'B' and resid 79 through 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 168 through 189 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 214 Processing helix chain 'B' and resid 219 through 240 Processing helix chain 'B' and resid 243 through 259 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 383 through 398 Processing helix chain 'B' and resid 405 through 427 Processing helix chain 'B' and resid 436 through 451 Processing helix chain 'B' and resid 453 through 463 Processing helix chain 'C' and resid 3 through 23 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 29 through 60 Processing helix chain 'C' and resid 65 through 102 Processing helix chain 'C' and resid 114 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 156 through 184 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 187 through 206 removed outlier: 3.631A pdb=" N LEU C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 231 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 236 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 3 through 5 No H-bonds generated for 'chain 'D' and resid 3 through 5' Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.602A pdb=" N PHE D 23 " --> pdb=" O TYR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 43 removed outlier: 4.031A pdb=" N ARG D 39 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLU D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 84 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 87 through 92 Processing sheet with id= A, 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= B, first strand: chain 'A' and resid 47 through 49 removed outlier: 6.270A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 248 through 250 Processing sheet with id= D, first strand: chain 'A' and resid 627 through 630 removed outlier: 3.802A pdb=" N ASP A 253 " --> pdb=" O ALA A 630 " (cutoff:3.500A) 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: 6.699A pdb=" N ILE A 412 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N MET A 378 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ARG A 414 " --> pdb=" O MET A 378 " (cutoff:3.500A) Processing sheet with id= E, 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) 511 hydrogen bonds defined for protein. 1509 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: 3.01 Time building geometry restraints manager: 5.19 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: 98.55 - 107.29: 446 107.29 - 116.03: 6727 116.03 - 124.77: 6309 124.77 - 133.51: 442 133.51 - 142.25: 42 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: 239 2.64 - 3.21: 10007 3.21 - 3.77: 16744 3.77 - 4.34: 21874 4.34 - 4.90: 35662 Nonbonded interactions: 84526 Sorted by model distance: nonbonded pdb=" O GLY A 504 " pdb=" OG1 THR A 505 " model vdw 2.079 2.440 nonbonded pdb=" OD1 ASN A 324 " pdb=" N VAL A 325 " model vdw 2.123 2.520 nonbonded pdb=" OE1 GLU A 186 " pdb=" OG1 THR A 189 " model vdw 2.209 2.440 nonbonded pdb=" O TYR A 645 " pdb=" OG SER A 646 " model vdw 2.228 2.440 nonbonded pdb=" O HIS A 222 " pdb=" OG SER A 651 " model vdw 2.234 2.440 ... (remaining 84521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.390 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: 1.940 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.540 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.470 ------------------------------------------------------------------------------- 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= 0.646 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 : 1.129 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: 0.2344 time to fit residues: 126.8331 Evaluate side-chains 265 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 208 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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: 1.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 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: 1.1186 ------------------------------------------------------------------------------- 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 478 ASN A 516 GLN A 531 ASN A 587 GLN A 606 GLN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4106 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10255 Z= 0.287 Angle : 0.806 10.853 13966 Z= 0.401 Chirality : 0.051 0.373 1657 Planarity : 0.005 0.050 1705 Dihedral : 15.311 106.312 1926 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.79 % Favored : 94.63 % Rotamer: Outliers : 8.78 % Allowed : 18.70 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.09 % 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: 0.82 (0.25), residues: 1211 helix: 2.42 (0.20), residues: 686 sheet: -1.44 (0.44), residues: 120 loop : -2.29 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 257 HIS 0.012 0.001 HIS A 553 PHE 0.038 0.002 PHE B 465 TYR 0.019 0.002 TYR A 569 ARG 0.008 0.001 ARG A 622 *********************** 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 334 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 242 time to evaluate : 1.109 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: 0.6424 (mtt180) cc_final: 0.6116 (mtm110) REVERT: A 80 GLU cc_start: 0.6648 (mm-30) cc_final: 0.6251 (tt0) REVERT: A 156 PHE cc_start: 0.6461 (m-80) cc_final: 0.6021 (m-80) REVERT: A 167 LEU cc_start: 0.6016 (tp) cc_final: 0.5739 (tt) REVERT: A 204 ASN cc_start: 0.7788 (m-40) cc_final: 0.6946 (t0) REVERT: A 210 PHE cc_start: 0.5259 (t80) cc_final: 0.4967 (t80) REVERT: A 213 CYS cc_start: 0.7066 (t) cc_final: 0.6466 (t) REVERT: A 280 THR cc_start: 0.5524 (OUTLIER) cc_final: 0.5071 (p) REVERT: A 281 ARG cc_start: 0.4145 (OUTLIER) cc_final: 0.3858 (ptm-80) REVERT: A 367 GLN cc_start: 0.4283 (OUTLIER) cc_final: 0.4031 (mm-40) REVERT: A 431 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6392 (mp) REVERT: A 464 ASN cc_start: 0.5921 (OUTLIER) cc_final: 0.5672 (t0) REVERT: A 541 ASP cc_start: 0.7711 (m-30) cc_final: 0.7328 (t0) REVERT: A 587 GLN cc_start: 0.7817 (tp40) cc_final: 0.7246 (pt0) REVERT: A 655 ASP cc_start: 0.6256 (m-30) cc_final: 0.5988 (t70) REVERT: A 693 LYS cc_start: 0.6028 (mmtp) cc_final: 0.5692 (mtpp) REVERT: B 167 ILE cc_start: 0.3547 (pp) cc_final: 0.3341 (tt) REVERT: B 446 TYR cc_start: 0.6355 (t80) cc_final: 0.6149 (t80) REVERT: C 96 LYS cc_start: 0.5584 (mttt) cc_final: 0.5244 (tptt) outliers start: 92 outliers final: 41 residues processed: 299 average time/residue: 0.2069 time to fit residues: 88.2995 Evaluate side-chains 247 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 201 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 174 GLU 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 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 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 632 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 152 ASP 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: 2.9990 chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 110 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN A 535 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4124 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10255 Z= 0.257 Angle : 0.718 10.125 13966 Z= 0.350 Chirality : 0.046 0.300 1657 Planarity : 0.005 0.047 1705 Dihedral : 12.194 97.835 1853 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.04 % Favored : 94.55 % Rotamer: Outliers : 7.35 % Allowed : 22.04 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1211 helix: 2.30 (0.20), residues: 670 sheet: -1.36 (0.44), residues: 125 loop : -2.13 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 257 HIS 0.006 0.001 HIS A 553 PHE 0.037 0.002 PHE B 465 TYR 0.018 0.002 TYR B 225 ARG 0.008 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 303 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 226 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6649 (mm-30) cc_final: 0.6249 (tt0) REVERT: A 94 TYR cc_start: 0.4746 (OUTLIER) cc_final: 0.4155 (m-80) REVERT: A 156 PHE cc_start: 0.6628 (OUTLIER) cc_final: 0.6229 (m-80) REVERT: A 167 LEU cc_start: 0.6006 (tp) cc_final: 0.5697 (tt) REVERT: A 248 CYS cc_start: 0.4055 (OUTLIER) cc_final: 0.3750 (m) REVERT: A 283 ASP cc_start: 0.5253 (p0) cc_final: 0.4851 (p0) REVERT: A 296 GLU cc_start: 0.5344 (tp30) cc_final: 0.5111 (tp30) REVERT: A 317 ASP cc_start: 0.6131 (t0) cc_final: 0.5928 (t0) REVERT: A 357 GLU cc_start: 0.7814 (tt0) cc_final: 0.7600 (tt0) REVERT: A 464 ASN cc_start: 0.5984 (OUTLIER) cc_final: 0.5730 (t0) REVERT: A 507 PHE cc_start: 0.6235 (m-10) cc_final: 0.5993 (m-80) REVERT: A 541 ASP cc_start: 0.7843 (m-30) cc_final: 0.7581 (t0) REVERT: A 587 GLN cc_start: 0.7835 (tp40) cc_final: 0.7232 (pt0) REVERT: A 591 LYS cc_start: 0.8400 (ttpp) cc_final: 0.8139 (mttm) REVERT: C 96 LYS cc_start: 0.5514 (mttt) cc_final: 0.5188 (tptt) REVERT: C 207 ASN cc_start: 0.4770 (OUTLIER) cc_final: 0.4487 (t0) REVERT: C 210 TYR cc_start: 0.5473 (m-80) cc_final: 0.4777 (m-80) outliers start: 77 outliers final: 39 residues processed: 280 average time/residue: 0.2028 time to fit residues: 83.0200 Evaluate side-chains 250 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 206 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU 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 111 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 364 GLU 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 516 GLN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 33 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 97 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 200 ASN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 GLN B 464 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4130 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10255 Z= 0.247 Angle : 0.686 10.830 13966 Z= 0.334 Chirality : 0.046 0.346 1657 Planarity : 0.004 0.045 1705 Dihedral : 11.212 99.717 1835 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.95 % Favored : 94.63 % Rotamer: Outliers : 6.97 % Allowed : 22.61 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1211 helix: 2.04 (0.20), residues: 668 sheet: -1.28 (0.45), residues: 119 loop : -2.07 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 257 HIS 0.006 0.001 HIS A 553 PHE 0.039 0.002 PHE B 465 TYR 0.017 0.002 TYR B 225 ARG 0.003 0.000 ARG A 622 *********************** 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 292 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 219 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6714 (mm-30) cc_final: 0.6300 (tt0) REVERT: A 94 TYR cc_start: 0.4448 (OUTLIER) cc_final: 0.3888 (m-80) REVERT: A 156 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.6401 (m-80) REVERT: A 167 LEU cc_start: 0.6018 (tp) cc_final: 0.5704 (tt) REVERT: A 248 CYS cc_start: 0.4466 (OUTLIER) cc_final: 0.3991 (m) REVERT: A 259 MET cc_start: 0.7381 (mmm) cc_final: 0.7177 (tpp) REVERT: A 317 ASP cc_start: 0.6207 (t0) cc_final: 0.5959 (t0) REVERT: A 357 GLU cc_start: 0.7521 (tt0) cc_final: 0.7266 (tt0) REVERT: A 364 GLU cc_start: 0.5362 (OUTLIER) cc_final: 0.4328 (mm-30) REVERT: A 464 ASN cc_start: 0.5975 (OUTLIER) cc_final: 0.5741 (t0) REVERT: A 541 ASP cc_start: 0.7900 (m-30) cc_final: 0.7657 (t0) REVERT: A 587 GLN cc_start: 0.7790 (tp40) cc_final: 0.7161 (pt0) REVERT: A 591 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8339 (mttm) REVERT: B 244 TRP cc_start: 0.5629 (OUTLIER) cc_final: 0.4265 (m-90) REVERT: C 96 LYS cc_start: 0.5504 (mttt) cc_final: 0.5171 (tptt) REVERT: C 210 TYR cc_start: 0.5535 (m-80) cc_final: 0.5205 (m-80) outliers start: 73 outliers final: 47 residues processed: 266 average time/residue: 0.1960 time to fit residues: 76.2515 Evaluate side-chains 255 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 202 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU 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 123 VAL 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 253 ASP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP 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 152 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 58 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 462 ASN A 516 GLN B 463 HIS B 464 GLN C 207 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4141 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10255 Z= 0.367 Angle : 0.725 9.816 13966 Z= 0.355 Chirality : 0.047 0.302 1657 Planarity : 0.004 0.048 1705 Dihedral : 10.724 111.813 1831 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.20 % Favored : 94.38 % Rotamer: Outliers : 7.73 % Allowed : 23.38 % 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: 0.26 (0.24), residues: 1211 helix: 1.75 (0.19), residues: 671 sheet: -1.16 (0.45), residues: 115 loop : -2.10 (0.29), residues: 425 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 0.043 0.002 PHE B 465 TYR 0.021 0.002 TYR B 225 ARG 0.004 0.001 ARG D 84 *********************** 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 285 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 204 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6320 (tt0) REVERT: A 94 TYR cc_start: 0.4148 (OUTLIER) cc_final: 0.3407 (m-80) REVERT: A 156 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.6360 (m-80) REVERT: A 167 LEU cc_start: 0.6352 (tp) cc_final: 0.6033 (tt) REVERT: A 221 MET cc_start: 0.7065 (mmt) cc_final: 0.6688 (mmt) REVERT: A 247 VAL cc_start: 0.4351 (p) cc_final: 0.4049 (p) REVERT: A 357 GLU cc_start: 0.7398 (tt0) cc_final: 0.7180 (tt0) REVERT: A 464 ASN cc_start: 0.6066 (OUTLIER) cc_final: 0.5852 (t0) REVERT: A 507 PHE cc_start: 0.5794 (m-80) cc_final: 0.5517 (m-80) REVERT: A 591 LYS cc_start: 0.8638 (ttpp) cc_final: 0.8349 (mttm) REVERT: A 695 ASP cc_start: 0.7176 (m-30) cc_final: 0.6764 (t70) REVERT: B 225 TYR cc_start: 0.4616 (m-80) cc_final: 0.4357 (m-80) REVERT: B 244 TRP cc_start: 0.5593 (OUTLIER) cc_final: 0.4322 (m-90) REVERT: C 96 LYS cc_start: 0.5521 (mttt) cc_final: 0.5177 (tptt) REVERT: C 210 TYR cc_start: 0.5643 (m-80) cc_final: 0.5309 (m-80) outliers start: 81 outliers final: 55 residues processed: 258 average time/residue: 0.1895 time to fit residues: 71.0941 Evaluate side-chains 257 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 198 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 53 LEU 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 217 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 444 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 164 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 67 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4135 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10255 Z= 0.216 Angle : 0.673 12.731 13966 Z= 0.325 Chirality : 0.044 0.311 1657 Planarity : 0.004 0.042 1705 Dihedral : 10.228 117.090 1831 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.12 % Favored : 94.55 % Rotamer: Outliers : 6.20 % Allowed : 25.67 % Favored : 68.13 % 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: 0.32 (0.24), residues: 1211 helix: 1.79 (0.19), residues: 672 sheet: -1.08 (0.46), residues: 115 loop : -2.08 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 174 HIS 0.005 0.001 HIS A 553 PHE 0.038 0.002 PHE B 465 TYR 0.020 0.001 TYR C 156 ARG 0.004 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 280 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 215 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6734 (mm-30) cc_final: 0.6305 (tt0) REVERT: A 156 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6735 (m-80) REVERT: A 167 LEU cc_start: 0.6277 (tp) cc_final: 0.5960 (tt) REVERT: A 221 MET cc_start: 0.7162 (mmt) cc_final: 0.6882 (mmt) REVERT: A 364 GLU cc_start: 0.5491 (OUTLIER) cc_final: 0.4530 (mm-30) REVERT: A 464 ASN cc_start: 0.6057 (OUTLIER) cc_final: 0.5833 (t0) REVERT: A 507 PHE cc_start: 0.5796 (m-80) cc_final: 0.5532 (m-80) REVERT: A 587 GLN cc_start: 0.6926 (mm110) cc_final: 0.6370 (pt0) REVERT: A 695 ASP cc_start: 0.7151 (m-30) cc_final: 0.6755 (t70) REVERT: B 225 TYR cc_start: 0.4602 (m-80) cc_final: 0.4351 (m-80) REVERT: B 244 TRP cc_start: 0.5474 (OUTLIER) cc_final: 0.4417 (m-90) REVERT: C 96 LYS cc_start: 0.5560 (mttt) cc_final: 0.5215 (tptt) REVERT: C 210 TYR cc_start: 0.5577 (m-80) cc_final: 0.5225 (m-80) outliers start: 65 outliers final: 42 residues processed: 255 average time/residue: 0.1988 time to fit residues: 73.3721 Evaluate side-chains 239 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 193 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 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 82 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 385 ASP 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 56 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4142 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 10255 Z= 0.309 Angle : 0.701 11.395 13966 Z= 0.339 Chirality : 0.046 0.346 1657 Planarity : 0.004 0.043 1705 Dihedral : 9.853 123.870 1829 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.53 % Favored : 94.22 % Rotamer: Outliers : 6.87 % Allowed : 24.90 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1211 helix: 1.57 (0.19), residues: 676 sheet: -1.12 (0.46), residues: 115 loop : -2.02 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 653 HIS 0.006 0.001 HIS A 553 PHE 0.041 0.002 PHE B 465 TYR 0.019 0.002 TYR B 225 ARG 0.003 0.000 ARG A 434 *********************** 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 273 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 201 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6304 (tt0) REVERT: A 94 TYR cc_start: 0.4285 (OUTLIER) cc_final: 0.3517 (m-80) REVERT: A 156 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: A 167 LEU cc_start: 0.6337 (tp) cc_final: 0.5978 (tt) REVERT: A 221 MET cc_start: 0.7062 (mmt) cc_final: 0.6712 (mmt) REVERT: A 464 ASN cc_start: 0.6182 (OUTLIER) cc_final: 0.5972 (t0) REVERT: A 507 PHE cc_start: 0.5827 (m-80) cc_final: 0.5581 (m-80) REVERT: A 559 SER cc_start: 0.5164 (OUTLIER) cc_final: 0.4922 (m) REVERT: A 695 ASP cc_start: 0.7148 (m-30) cc_final: 0.6749 (t70) REVERT: B 225 TYR cc_start: 0.4465 (m-80) cc_final: 0.4120 (m-80) REVERT: B 244 TRP cc_start: 0.5443 (OUTLIER) cc_final: 0.4151 (m-90) REVERT: C 96 LYS cc_start: 0.5568 (mttt) cc_final: 0.5221 (tptt) REVERT: C 210 TYR cc_start: 0.5701 (m-80) cc_final: 0.5369 (m-80) outliers start: 72 outliers final: 57 residues processed: 251 average time/residue: 0.1875 time to fit residues: 68.7804 Evaluate side-chains 258 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 196 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 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 217 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 SER 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 82 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 423 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 93 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 67 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 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: 9.9990 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10255 Z= 0.299 Angle : 0.693 10.098 13966 Z= 0.339 Chirality : 0.046 0.354 1657 Planarity : 0.004 0.043 1705 Dihedral : 9.733 130.064 1829 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.45 % Favored : 94.30 % Rotamer: Outliers : 7.25 % Allowed : 24.62 % Favored : 68.13 % 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: 0.09 (0.24), residues: 1211 helix: 1.46 (0.19), residues: 676 sheet: -1.14 (0.46), residues: 115 loop : -1.96 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 653 HIS 0.006 0.001 HIS A 553 PHE 0.037 0.002 PHE B 465 TYR 0.021 0.002 TYR B 225 ARG 0.002 0.000 ARG A 622 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 204 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6749 (mm-30) cc_final: 0.6297 (tt0) REVERT: A 94 TYR cc_start: 0.4363 (OUTLIER) cc_final: 0.3554 (m-80) REVERT: A 156 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6786 (m-80) REVERT: A 167 LEU cc_start: 0.6334 (tp) cc_final: 0.5972 (tt) REVERT: A 259 MET cc_start: 0.7417 (mmm) cc_final: 0.6662 (mmm) REVERT: A 507 PHE cc_start: 0.6052 (m-80) cc_final: 0.5801 (m-80) REVERT: A 559 SER cc_start: 0.5387 (OUTLIER) cc_final: 0.5116 (m) REVERT: A 695 ASP cc_start: 0.7144 (m-30) cc_final: 0.6765 (t70) REVERT: B 225 TYR cc_start: 0.4460 (m-80) cc_final: 0.4105 (m-80) REVERT: B 244 TRP cc_start: 0.5426 (OUTLIER) cc_final: 0.4126 (m-90) REVERT: C 210 TYR cc_start: 0.5617 (m-80) cc_final: 0.5161 (m-80) outliers start: 76 outliers final: 59 residues processed: 257 average time/residue: 0.2000 time to fit residues: 75.6518 Evaluate side-chains 263 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 200 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 53 LEU 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 217 LEU 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 364 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 SER 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 665 SER Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 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 385 ASP Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 93 LEU 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 33 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 67 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 587 GLN C 207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4150 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10255 Z= 0.260 Angle : 0.684 9.788 13966 Z= 0.334 Chirality : 0.046 0.379 1657 Planarity : 0.004 0.048 1705 Dihedral : 9.537 131.269 1827 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.62 % Favored : 94.14 % Rotamer: Outliers : 6.39 % Allowed : 26.05 % Favored : 67.56 % 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: 0.11 (0.24), residues: 1211 helix: 1.48 (0.19), residues: 673 sheet: -1.19 (0.49), residues: 103 loop : -1.91 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 653 HIS 0.005 0.001 HIS A 553 PHE 0.043 0.002 PHE B 465 TYR 0.018 0.001 TYR B 225 ARG 0.003 0.000 ARG A 583 *********************** 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 278 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 211 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6286 (tt0) REVERT: A 94 TYR cc_start: 0.4237 (OUTLIER) cc_final: 0.3413 (m-80) REVERT: A 156 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6898 (m-80) REVERT: A 167 LEU cc_start: 0.6315 (tp) cc_final: 0.5952 (tt) REVERT: A 305 GLN cc_start: 0.6120 (tp40) cc_final: 0.5816 (tt0) REVERT: A 507 PHE cc_start: 0.6131 (m-80) cc_final: 0.5883 (m-80) REVERT: A 559 SER cc_start: 0.5470 (OUTLIER) cc_final: 0.5023 (t) REVERT: A 695 ASP cc_start: 0.7138 (m-30) cc_final: 0.6756 (t70) REVERT: B 222 GLN cc_start: 0.6108 (tt0) cc_final: 0.5883 (tp40) REVERT: B 225 TYR cc_start: 0.4461 (m-80) cc_final: 0.4104 (m-80) REVERT: B 244 TRP cc_start: 0.5307 (OUTLIER) cc_final: 0.4232 (m-90) REVERT: C 210 TYR cc_start: 0.5732 (m-80) cc_final: 0.5475 (m-80) outliers start: 67 outliers final: 57 residues processed: 254 average time/residue: 0.1897 time to fit residues: 70.3364 Evaluate side-chains 260 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 199 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 53 LEU 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 217 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 SER 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 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 385 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 67 TRP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 0.0980 chunk 120 optimal weight: 0.6980 chunk 110 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4149 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10255 Z= 0.219 Angle : 0.675 9.522 13966 Z= 0.327 Chirality : 0.045 0.440 1657 Planarity : 0.004 0.050 1705 Dihedral : 9.428 132.132 1827 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.70 % Favored : 94.05 % Rotamer: Outliers : 5.53 % Allowed : 26.53 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1211 helix: 1.51 (0.19), residues: 673 sheet: -1.14 (0.49), residues: 103 loop : -1.86 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 653 HIS 0.005 0.001 HIS B 463 PHE 0.043 0.002 PHE B 465 TYR 0.017 0.001 TYR B 225 ARG 0.002 0.000 ARG A 434 ********************** 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 283 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 225 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6277 (tt0) REVERT: A 94 TYR cc_start: 0.4247 (OUTLIER) cc_final: 0.3434 (m-80) REVERT: A 156 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6919 (m-80) REVERT: A 167 LEU cc_start: 0.6384 (tp) cc_final: 0.6036 (tt) REVERT: A 305 GLN cc_start: 0.6258 (tp40) cc_final: 0.5857 (tt0) REVERT: A 507 PHE cc_start: 0.6079 (m-80) cc_final: 0.5876 (m-80) REVERT: A 559 SER cc_start: 0.5505 (OUTLIER) cc_final: 0.4937 (t) REVERT: B 222 GLN cc_start: 0.6136 (tt0) cc_final: 0.5932 (tp40) REVERT: B 225 TYR cc_start: 0.4426 (m-80) cc_final: 0.4075 (m-80) REVERT: B 244 TRP cc_start: 0.5183 (OUTLIER) cc_final: 0.4137 (m-90) REVERT: C 174 TRP cc_start: 0.4970 (m-10) cc_final: 0.4513 (m-10) outliers start: 58 outliers final: 48 residues processed: 259 average time/residue: 0.1872 time to fit residues: 71.2488 Evaluate side-chains 259 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 207 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 147 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 SER 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 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 385 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain 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 137 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 12 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 84 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS B 464 GLN C 207 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.111776 restraints weight = 15445.099| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.47 r_work: 0.3133 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10255 Z= 0.220 Angle : 0.668 9.515 13966 Z= 0.324 Chirality : 0.045 0.481 1657 Planarity : 0.004 0.052 1705 Dihedral : 9.261 133.020 1827 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.86 % Favored : 93.89 % Rotamer: Outliers : 5.25 % Allowed : 27.58 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (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: 0.19 (0.24), residues: 1211 helix: 1.53 (0.19), residues: 673 sheet: -1.11 (0.50), residues: 103 loop : -1.86 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 653 HIS 0.007 0.001 HIS B 463 PHE 0.043 0.002 PHE B 465 TYR 0.017 0.001 TYR C 156 ARG 0.003 0.000 ARG A 434 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2398.29 seconds wall clock time: 43 minutes 48.30 seconds (2628.30 seconds total)