Starting phenix.real_space_refine on Wed Sep 17 10:30:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vse_43497/09_2025/8vse_43497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vse_43497/09_2025/8vse_43497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vse_43497/09_2025/8vse_43497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vse_43497/09_2025/8vse_43497.map" model { file = "/net/cci-nas-00/data/ceres_data/8vse_43497/09_2025/8vse_43497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vse_43497/09_2025/8vse_43497.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 5042 2.51 5 N 1360 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8043 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2826 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2826 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 333} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2114 Classifications: {'peptide': 261} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 242} Chain breaks: 1 Chain: "L" 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: "D" 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: "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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.08, per 1000 atoms: 0.26 Number of scatterers: 8043 At special positions: 0 Unit cell: (79.222, 109.23, 182.451, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 1590 8.00 N 1360 7.00 C 5042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 258 " - pdb=" SG CYS A 263 " distance=2.03 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 342 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 423 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 286 " distance=2.03 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 423 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 48 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 601 " - " ASN A 419 " " NAG A 602 " - " ASN A 468 " " NAG A 603 " - " ASN A 529 " " NAG B 601 " - " ASN B 468 " " NAG C 401 " - " ASN C 6 " " NAG D 1 " - " ASN C 59 " " NAG E 1 " - " ASN C 12 " " NAG F 1 " - " ASN C 35 " " NAG G 1 " - " ASN C 52 " " NAG H 1 " - " ASN C 107 " " NAG I 1 " - " ASN C 154 " " NAG L 1 " - " ASN A 378 " Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 325.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 24 sheets defined 3.5% alpha, 39.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.769A pdb=" N LYS A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 230 " --> pdb=" O CYS A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 230' Processing helix chain 'A' and resid 311 through 315 removed outlier: 3.564A pdb=" N ALA A 315 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 136 through 139 Processing helix chain 'C' and resid 300 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 240 removed outlier: 6.672A pdb=" N PHE A 246 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 270 " --> pdb=" O PHE A 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 281 removed outlier: 4.005A pdb=" N LYS A 291 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA4, first strand: chain 'A' and resid 345 through 347 removed outlier: 3.781A pdb=" N THR A 377 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TYR A 371 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LYS A 375 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 394 through 399 removed outlier: 5.598A pdb=" N ILE A 395 " --> pdb=" O ASN A 411 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN A 411 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 Processing sheet with id=AA7, first strand: chain 'A' and resid 461 through 462 Processing sheet with id=AA8, first strand: chain 'A' and resid 487 through 493 removed outlier: 5.259A pdb=" N ASN A 488 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG A 504 " --> pdb=" O ASN A 488 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 532 Processing sheet with id=AB1, first strand: chain 'B' and resid 235 through 240 removed outlier: 7.177A pdb=" N PHE B 246 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASN B 270 " --> pdb=" O PHE B 246 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 276 through 281 Processing sheet with id=AB3, first strand: chain 'B' and resid 304 through 308 Processing sheet with id=AB4, first strand: chain 'B' and resid 345 through 348 removed outlier: 5.908A pdb=" N TYR B 371 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LYS B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 394 through 399 removed outlier: 5.706A pdb=" N ILE B 395 " --> pdb=" O ASN B 411 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN B 411 " --> pdb=" O ILE B 395 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 430 through 436 Processing sheet with id=AB7, first strand: chain 'B' and resid 430 through 436 Processing sheet with id=AB8, first strand: chain 'B' and resid 491 through 493 Processing sheet with id=AB9, first strand: chain 'B' and resid 526 through 532 Processing sheet with id=AC1, first strand: chain 'C' and resid 2 through 5 removed outlier: 6.850A pdb=" N HIS C 3 " --> pdb=" O LYS C 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 13 through 15 Processing sheet with id=AC3, first strand: chain 'C' and resid 98 through 103 removed outlier: 7.263A pdb=" N ASN C 122 " --> pdb=" O LYS C 127 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS C 127 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 133 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 108 through 111 Processing sheet with id=AC5, first strand: chain 'C' and resid 247 through 252 Processing sheet with id=AC6, first strand: chain 'C' and resid 257 through 260 275 hydrogen bonds defined for protein. 696 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: 0.90 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2575 1.34 - 1.46: 1829 1.46 - 1.58: 3774 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 8242 Sorted by residual: bond pdb=" C PRO A 298 " pdb=" N PRO A 299 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.68e+00 bond pdb=" CA PRO A 298 " pdb=" C PRO A 298 " ideal model delta sigma weight residual 1.517 1.527 -0.010 9.30e-03 1.16e+04 1.14e+00 bond pdb=" C3 NAG I 1 " pdb=" C4 NAG I 1 " ideal model delta sigma weight residual 1.524 1.542 -0.018 2.00e-02 2.50e+03 8.42e-01 bond pdb=" N PHE A 420 " pdb=" CA PHE A 420 " ideal model delta sigma weight residual 1.461 1.473 -0.012 1.38e-02 5.25e+03 7.73e-01 bond pdb=" C2 NAG F 2 " pdb=" N2 NAG F 2 " ideal model delta sigma weight residual 1.439 1.455 -0.016 2.00e-02 2.50e+03 6.24e-01 ... (remaining 8237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11062 1.92 - 3.84: 117 3.84 - 5.76: 13 5.76 - 7.68: 4 7.68 - 9.60: 2 Bond angle restraints: 11198 Sorted by residual: angle pdb=" N PRO A 298 " pdb=" CA PRO A 298 " pdb=" C PRO A 298 " ideal model delta sigma weight residual 110.70 115.67 -4.97 1.22e+00 6.72e-01 1.66e+01 angle pdb=" C HIS A 418 " pdb=" N ASN A 419 " pdb=" CA ASN A 419 " ideal model delta sigma weight residual 121.53 115.93 5.60 1.53e+00 4.27e-01 1.34e+01 angle pdb=" CA PRO A 298 " pdb=" C PRO A 298 " pdb=" N PRO A 299 " ideal model delta sigma weight residual 117.93 122.01 -4.08 1.20e+00 6.94e-01 1.16e+01 angle pdb=" N ASN A 419 " pdb=" CA ASN A 419 " pdb=" C ASN A 419 " ideal model delta sigma weight residual 110.41 114.22 -3.81 1.18e+00 7.18e-01 1.04e+01 angle pdb=" C2 NAG F 2 " pdb=" N2 NAG F 2 " pdb=" C7 NAG F 2 " ideal model delta sigma weight residual 124.56 134.16 -9.60 3.00e+00 1.11e-01 1.02e+01 ... (remaining 11193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 4813 11.82 - 23.65: 306 23.65 - 35.47: 77 35.47 - 47.30: 26 47.30 - 59.12: 22 Dihedral angle restraints: 5244 sinusoidal: 2398 harmonic: 2846 Sorted by residual: dihedral pdb=" CA ASN A 419 " pdb=" C ASN A 419 " pdb=" N PHE A 420 " pdb=" CA PHE A 420 " ideal model delta harmonic sigma weight residual 180.00 149.38 30.62 0 5.00e+00 4.00e-02 3.75e+01 dihedral pdb=" CA VAL A 301 " pdb=" C VAL A 301 " pdb=" N GLU A 302 " pdb=" CA GLU A 302 " ideal model delta harmonic sigma weight residual 180.00 -156.61 -23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA ASN C 154 " pdb=" C ASN C 154 " pdb=" N PHE C 155 " pdb=" CA PHE C 155 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1108 0.057 - 0.113: 141 0.113 - 0.170: 20 0.170 - 0.226: 3 0.226 - 0.283: 2 Chirality restraints: 1274 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 419 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C2 NAG F 2 " pdb=" C1 NAG F 2 " pdb=" C3 NAG F 2 " pdb=" N2 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.23 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN C 12 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1271 not shown) Planarity restraints: 1444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 297 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 298 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 482 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO A 483 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 483 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 483 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 420 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" C PHE A 420 " -0.017 2.00e-02 2.50e+03 pdb=" O PHE A 420 " 0.007 2.00e-02 2.50e+03 pdb=" N THR A 421 " 0.006 2.00e-02 2.50e+03 ... (remaining 1441 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2224 2.82 - 3.34: 6805 3.34 - 3.86: 12941 3.86 - 4.38: 14740 4.38 - 4.90: 25237 Nonbonded interactions: 61947 Sorted by model distance: nonbonded pdb=" O GLN B 466 " pdb=" O6 NAG B 601 " model vdw 2.297 3.040 nonbonded pdb=" OE2 GLU A 358 " pdb=" OH TYR A 363 " model vdw 2.297 3.040 nonbonded pdb=" O PRO B 506 " pdb=" NH1 ARG B 509 " model vdw 2.301 3.120 nonbonded pdb=" OG SER B 495 " pdb=" OG SER B 498 " model vdw 2.305 3.040 nonbonded pdb=" O PRO C 114 " pdb=" ND2 ASN C 165 " model vdw 2.306 3.120 ... (remaining 61942 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 224 through 601) selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' } 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 group one per residue 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.060 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 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 : 0.002 0.038 8279 Z= 0.087 Angle : 0.559 12.822 11292 Z= 0.264 Chirality : 0.043 0.283 1274 Planarity : 0.003 0.035 1432 Dihedral : 9.298 59.122 3353 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.48 % Allowed : 5.02 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.28), residues: 955 helix: -0.76 (2.12), residues: 6 sheet: 1.76 (0.25), residues: 438 loop : -0.12 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 399 TYR 0.008 0.001 TYR B 424 PHE 0.006 0.001 PHE B 376 TRP 0.005 0.001 TRP C 10 HIS 0.002 0.000 HIS B 500 Details of bonding type rmsd covalent geometry : bond 0.00186 ( 8242) covalent geometry : angle 0.50880 (11198) SS BOND : bond 0.00141 ( 17) SS BOND : angle 0.52645 ( 34) hydrogen bonds : bond 0.08508 ( 261) hydrogen bonds : angle 4.72091 ( 696) link_BETA1-4 : bond 0.00922 ( 8) link_BETA1-4 : angle 3.37349 ( 24) link_NAG-ASN : bond 0.00264 ( 12) link_NAG-ASN : angle 3.09779 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.5644 (OUTLIER) cc_final: 0.5430 (tt) REVERT: A 389 SER cc_start: 0.7725 (m) cc_final: 0.7515 (p) REVERT: A 468 ASN cc_start: 0.7208 (OUTLIER) cc_final: 0.6828 (m-40) REVERT: C 153 VAL cc_start: 0.7546 (t) cc_final: 0.7238 (p) REVERT: C 260 VAL cc_start: 0.8593 (t) cc_final: 0.8299 (p) REVERT: C 319 TYR cc_start: 0.7591 (m-80) cc_final: 0.7053 (m-80) outliers start: 13 outliers final: 4 residues processed: 158 average time/residue: 0.1404 time to fit residues: 27.4040 Evaluate side-chains 68 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 178 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 532 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.092994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.075658 restraints weight = 38946.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.077711 restraints weight = 21548.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.079025 restraints weight = 14475.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.079913 restraints weight = 11047.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.080441 restraints weight = 9150.728| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8279 Z= 0.161 Angle : 0.727 13.589 11292 Z= 0.349 Chirality : 0.045 0.308 1274 Planarity : 0.004 0.044 1432 Dihedral : 8.040 58.406 1463 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.28 % Allowed : 9.81 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.28), residues: 955 helix: -0.41 (2.15), residues: 6 sheet: 1.66 (0.25), residues: 458 loop : -0.14 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 509 TYR 0.019 0.001 TYR C 174 PHE 0.015 0.002 PHE B 347 TRP 0.010 0.001 TRP B 487 HIS 0.014 0.001 HIS B 532 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8242) covalent geometry : angle 0.67795 (11198) SS BOND : bond 0.00351 ( 17) SS BOND : angle 2.00012 ( 34) hydrogen bonds : bond 0.03199 ( 261) hydrogen bonds : angle 4.75613 ( 696) link_BETA1-4 : bond 0.00709 ( 8) link_BETA1-4 : angle 3.27909 ( 24) link_NAG-ASN : bond 0.00275 ( 12) link_NAG-ASN : angle 3.47268 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7264 (tp) REVERT: A 389 SER cc_start: 0.8220 (m) cc_final: 0.7826 (p) REVERT: A 409 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8424 (p) REVERT: B 559 TYR cc_start: 0.7800 (m-80) cc_final: 0.7491 (m-10) REVERT: C 104 MET cc_start: 0.7821 (mtm) cc_final: 0.6695 (tpt) REVERT: C 260 VAL cc_start: 0.8984 (t) cc_final: 0.8737 (p) outliers start: 20 outliers final: 10 residues processed: 89 average time/residue: 0.1191 time to fit residues: 13.5415 Evaluate side-chains 57 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 178 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.095057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.076513 restraints weight = 46185.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.078210 restraints weight = 26743.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.079292 restraints weight = 18891.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.080151 restraints weight = 15173.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.080502 restraints weight = 13076.828| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 8279 Z= 0.286 Angle : 0.799 13.368 11292 Z= 0.393 Chirality : 0.047 0.315 1274 Planarity : 0.005 0.049 1432 Dihedral : 8.318 59.344 1459 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.28 % Allowed : 11.74 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.28), residues: 955 helix: -0.72 (1.94), residues: 6 sheet: 1.15 (0.24), residues: 462 loop : -0.43 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 509 TYR 0.017 0.002 TYR A 548 PHE 0.028 0.003 PHE B 420 TRP 0.011 0.002 TRP B 487 HIS 0.007 0.002 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 8242) covalent geometry : angle 0.74714 (11198) SS BOND : bond 0.00503 ( 17) SS BOND : angle 1.11757 ( 34) hydrogen bonds : bond 0.04149 ( 261) hydrogen bonds : angle 5.09785 ( 696) link_BETA1-4 : bond 0.00491 ( 8) link_BETA1-4 : angle 3.77312 ( 24) link_NAG-ASN : bond 0.00817 ( 12) link_NAG-ASN : angle 4.00319 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8763 (t) REVERT: A 415 ARG cc_start: 0.7632 (ttm110) cc_final: 0.6952 (ttm110) REVERT: B 327 GLU cc_start: 0.7755 (pm20) cc_final: 0.7380 (pm20) REVERT: B 349 ASN cc_start: 0.7765 (t0) cc_final: 0.7514 (t0) REVERT: B 489 MET cc_start: 0.7949 (ttp) cc_final: 0.7687 (tpt) REVERT: C 104 MET cc_start: 0.8179 (mtm) cc_final: 0.6855 (tpt) REVERT: C 128 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6812 (t80) outliers start: 20 outliers final: 15 residues processed: 71 average time/residue: 0.1213 time to fit residues: 11.3696 Evaluate side-chains 60 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 532 HIS Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 6 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 7 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 HIS ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.089389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.071231 restraints weight = 41004.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.073400 restraints weight = 22278.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.074781 restraints weight = 14811.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.075693 restraints weight = 11330.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.076339 restraints weight = 9368.844| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8279 Z= 0.197 Angle : 0.715 13.953 11292 Z= 0.348 Chirality : 0.045 0.302 1274 Planarity : 0.004 0.048 1432 Dihedral : 8.251 59.128 1459 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.17 % Allowed : 11.63 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.28), residues: 955 helix: -0.56 (2.01), residues: 6 sheet: 0.98 (0.24), residues: 471 loop : -0.46 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 504 TYR 0.011 0.001 TYR A 548 PHE 0.013 0.002 PHE B 420 TRP 0.016 0.002 TRP B 487 HIS 0.006 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 8242) covalent geometry : angle 0.66096 (11198) SS BOND : bond 0.00293 ( 17) SS BOND : angle 0.84607 ( 34) hydrogen bonds : bond 0.03642 ( 261) hydrogen bonds : angle 5.04546 ( 696) link_BETA1-4 : bond 0.00784 ( 8) link_BETA1-4 : angle 3.84209 ( 24) link_NAG-ASN : bond 0.00454 ( 12) link_NAG-ASN : angle 3.72441 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7804 (tptp) REVERT: B 349 ASN cc_start: 0.7823 (t0) cc_final: 0.7549 (t0) REVERT: B 489 MET cc_start: 0.7814 (ttp) cc_final: 0.7578 (tpt) REVERT: C 104 MET cc_start: 0.7541 (mtm) cc_final: 0.6909 (tpt) REVERT: C 124 ASP cc_start: 0.8187 (t70) cc_final: 0.7951 (t0) REVERT: C 128 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6675 (t80) outliers start: 19 outliers final: 10 residues processed: 65 average time/residue: 0.1007 time to fit residues: 9.2002 Evaluate side-chains 53 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 94 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 30.0000 chunk 95 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 30.0000 chunk 30 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.088415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.071215 restraints weight = 39511.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.073127 restraints weight = 21597.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.074373 restraints weight = 14551.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.075150 restraints weight = 11132.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.075639 restraints weight = 9338.721| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8279 Z= 0.182 Angle : 0.700 13.970 11292 Z= 0.339 Chirality : 0.046 0.299 1274 Planarity : 0.004 0.048 1432 Dihedral : 8.272 58.467 1458 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.17 % Allowed : 12.09 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.28), residues: 955 helix: -0.42 (2.03), residues: 6 sheet: 0.88 (0.24), residues: 466 loop : -0.46 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 284 TYR 0.010 0.001 TYR A 548 PHE 0.012 0.002 PHE B 420 TRP 0.005 0.001 TRP C 270 HIS 0.006 0.001 HIS B 532 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8242) covalent geometry : angle 0.64324 (11198) SS BOND : bond 0.00435 ( 17) SS BOND : angle 1.17106 ( 34) hydrogen bonds : bond 0.03543 ( 261) hydrogen bonds : angle 5.06128 ( 696) link_BETA1-4 : bond 0.00784 ( 8) link_BETA1-4 : angle 3.86288 ( 24) link_NAG-ASN : bond 0.00409 ( 12) link_NAG-ASN : angle 3.71509 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 SER cc_start: 0.5716 (OUTLIER) cc_final: 0.4934 (t) REVERT: B 448 LYS cc_start: 0.9103 (tppt) cc_final: 0.8799 (tppt) REVERT: B 489 MET cc_start: 0.7846 (ttp) cc_final: 0.7477 (tpt) REVERT: C 128 PHE cc_start: 0.7187 (OUTLIER) cc_final: 0.6536 (t80) outliers start: 19 outliers final: 11 residues processed: 63 average time/residue: 0.1191 time to fit residues: 10.0948 Evaluate side-chains 55 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.089128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.072197 restraints weight = 39324.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.074061 restraints weight = 21583.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.075235 restraints weight = 14492.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.076059 restraints weight = 11202.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.076547 restraints weight = 9362.432| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8279 Z= 0.145 Angle : 0.689 14.279 11292 Z= 0.332 Chirality : 0.045 0.299 1274 Planarity : 0.005 0.055 1432 Dihedral : 8.190 57.729 1458 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.48 % Allowed : 13.68 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.28), residues: 955 helix: -0.42 (2.07), residues: 6 sheet: 1.00 (0.24), residues: 461 loop : -0.47 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 507 TYR 0.010 0.001 TYR B 424 PHE 0.012 0.001 PHE C 155 TRP 0.017 0.002 TRP B 487 HIS 0.023 0.001 HIS B 532 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8242) covalent geometry : angle 0.63529 (11198) SS BOND : bond 0.00219 ( 17) SS BOND : angle 0.70951 ( 34) hydrogen bonds : bond 0.03275 ( 261) hydrogen bonds : angle 5.01958 ( 696) link_BETA1-4 : bond 0.00946 ( 8) link_BETA1-4 : angle 3.81254 ( 24) link_NAG-ASN : bond 0.00249 ( 12) link_NAG-ASN : angle 3.62354 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 448 LYS cc_start: 0.9093 (tppt) cc_final: 0.8788 (tppt) REVERT: B 489 MET cc_start: 0.7852 (ttp) cc_final: 0.7536 (tpt) REVERT: C 104 MET cc_start: 0.7091 (ptp) cc_final: 0.6579 (tpt) REVERT: C 124 ASP cc_start: 0.8227 (t70) cc_final: 0.7857 (t0) REVERT: C 128 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6415 (t80) REVERT: C 320 ARG cc_start: 0.7346 (mtm-85) cc_final: 0.7118 (ttm110) outliers start: 13 outliers final: 10 residues processed: 55 average time/residue: 0.0997 time to fit residues: 7.8484 Evaluate side-chains 47 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 0.1980 chunk 91 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.096141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.078271 restraints weight = 46971.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.079921 restraints weight = 26390.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.081151 restraints weight = 18422.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.081829 restraints weight = 14508.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.082375 restraints weight = 12548.664| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8279 Z= 0.118 Angle : 0.657 14.170 11292 Z= 0.314 Chirality : 0.045 0.303 1274 Planarity : 0.004 0.046 1432 Dihedral : 8.090 57.216 1458 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.94 % Allowed : 13.11 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.28), residues: 955 helix: -0.22 (2.13), residues: 6 sheet: 1.04 (0.24), residues: 461 loop : -0.48 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 320 TYR 0.011 0.001 TYR B 553 PHE 0.016 0.001 PHE C 155 TRP 0.006 0.001 TRP C 120 HIS 0.015 0.001 HIS B 532 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8242) covalent geometry : angle 0.60302 (11198) SS BOND : bond 0.00182 ( 17) SS BOND : angle 0.64321 ( 34) hydrogen bonds : bond 0.03112 ( 261) hydrogen bonds : angle 4.98242 ( 696) link_BETA1-4 : bond 0.00953 ( 8) link_BETA1-4 : angle 3.71587 ( 24) link_NAG-ASN : bond 0.00205 ( 12) link_NAG-ASN : angle 3.53596 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 448 LYS cc_start: 0.9098 (tppt) cc_final: 0.8796 (tppt) REVERT: B 489 MET cc_start: 0.7822 (ttp) cc_final: 0.7526 (tpt) REVERT: C 104 MET cc_start: 0.7268 (ptp) cc_final: 0.6584 (tpt) REVERT: C 128 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.6321 (t80) outliers start: 17 outliers final: 12 residues processed: 57 average time/residue: 0.1001 time to fit residues: 8.1038 Evaluate side-chains 50 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 0.0870 chunk 44 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.087057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.069967 restraints weight = 40508.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.071833 restraints weight = 22192.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.073015 restraints weight = 14998.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.073727 restraints weight = 11579.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.074262 restraints weight = 9846.514| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8279 Z= 0.230 Angle : 0.739 13.920 11292 Z= 0.357 Chirality : 0.046 0.283 1274 Planarity : 0.004 0.051 1432 Dihedral : 8.294 58.290 1458 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.82 % Allowed : 14.03 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.27), residues: 955 helix: -0.36 (2.00), residues: 6 sheet: 0.79 (0.24), residues: 452 loop : -0.63 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 284 TYR 0.013 0.002 TYR C 69 PHE 0.017 0.002 PHE B 376 TRP 0.010 0.002 TRP A 410 HIS 0.011 0.001 HIS B 532 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 8242) covalent geometry : angle 0.68550 (11198) SS BOND : bond 0.00368 ( 17) SS BOND : angle 0.75376 ( 34) hydrogen bonds : bond 0.03820 ( 261) hydrogen bonds : angle 5.21200 ( 696) link_BETA1-4 : bond 0.00765 ( 8) link_BETA1-4 : angle 3.88799 ( 24) link_NAG-ASN : bond 0.00509 ( 12) link_NAG-ASN : angle 3.78175 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8572 (tm-30) REVERT: B 489 MET cc_start: 0.7750 (ttp) cc_final: 0.7500 (tpt) REVERT: C 128 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6605 (t80) outliers start: 16 outliers final: 12 residues processed: 54 average time/residue: 0.0939 time to fit residues: 7.4049 Evaluate side-chains 51 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.0370 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 ASN ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.088057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.071200 restraints weight = 39400.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.073115 restraints weight = 21488.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.074351 restraints weight = 14472.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.075102 restraints weight = 11076.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.075607 restraints weight = 9321.849| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8279 Z= 0.154 Angle : 0.700 14.362 11292 Z= 0.336 Chirality : 0.045 0.278 1274 Planarity : 0.004 0.045 1432 Dihedral : 8.249 57.477 1458 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.71 % Allowed : 14.60 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.28), residues: 955 helix: -0.42 (2.01), residues: 6 sheet: 0.83 (0.24), residues: 464 loop : -0.57 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 415 TYR 0.014 0.001 TYR B 548 PHE 0.013 0.002 PHE A 417 TRP 0.008 0.001 TRP C 270 HIS 0.009 0.001 HIS B 532 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8242) covalent geometry : angle 0.64755 (11198) SS BOND : bond 0.00242 ( 17) SS BOND : angle 0.62206 ( 34) hydrogen bonds : bond 0.03309 ( 261) hydrogen bonds : angle 5.17828 ( 696) link_BETA1-4 : bond 0.00963 ( 8) link_BETA1-4 : angle 3.83081 ( 24) link_NAG-ASN : bond 0.00246 ( 12) link_NAG-ASN : angle 3.61895 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8555 (tm-30) REVERT: A 372 ASN cc_start: 0.7984 (m-40) cc_final: 0.7050 (t0) REVERT: A 499 MET cc_start: 0.7141 (tpp) cc_final: 0.6715 (tpp) REVERT: B 489 MET cc_start: 0.7716 (ttp) cc_final: 0.7492 (tpt) REVERT: C 128 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.6430 (t80) outliers start: 15 outliers final: 11 residues processed: 57 average time/residue: 0.1047 time to fit residues: 8.3905 Evaluate side-chains 47 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 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 361 HIS ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.085936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.068768 restraints weight = 40569.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.070592 restraints weight = 22251.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.071786 restraints weight = 14993.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.072562 restraints weight = 11540.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.073023 restraints weight = 9700.980| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 8279 Z= 0.260 Angle : 0.788 13.972 11292 Z= 0.385 Chirality : 0.046 0.270 1274 Planarity : 0.005 0.046 1432 Dihedral : 8.583 58.818 1458 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.48 % Allowed : 14.60 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.27), residues: 955 helix: -0.64 (1.87), residues: 6 sheet: 0.62 (0.24), residues: 451 loop : -0.85 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 415 TYR 0.023 0.002 TYR B 548 PHE 0.020 0.002 PHE B 376 TRP 0.013 0.002 TRP A 410 HIS 0.007 0.001 HIS B 532 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 8242) covalent geometry : angle 0.73624 (11198) SS BOND : bond 0.00395 ( 17) SS BOND : angle 0.78371 ( 34) hydrogen bonds : bond 0.04079 ( 261) hydrogen bonds : angle 5.46881 ( 696) link_BETA1-4 : bond 0.00832 ( 8) link_BETA1-4 : angle 3.94975 ( 24) link_NAG-ASN : bond 0.00575 ( 12) link_NAG-ASN : angle 3.87722 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8630 (tm-30) REVERT: A 499 MET cc_start: 0.7071 (tpp) cc_final: 0.6839 (tpp) REVERT: B 489 MET cc_start: 0.7891 (ttp) cc_final: 0.7525 (tpt) REVERT: C 128 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.6728 (t80) outliers start: 13 outliers final: 11 residues processed: 50 average time/residue: 0.0927 time to fit residues: 6.7808 Evaluate side-chains 49 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 45 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.088084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.071456 restraints weight = 38935.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.073299 restraints weight = 21118.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.074441 restraints weight = 14109.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.075264 restraints weight = 10865.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.075740 restraints weight = 9050.655| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8279 Z= 0.128 Angle : 0.708 14.459 11292 Z= 0.341 Chirality : 0.045 0.272 1274 Planarity : 0.004 0.045 1432 Dihedral : 8.398 58.233 1458 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.48 % Allowed : 14.82 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.28), residues: 955 helix: -0.40 (2.04), residues: 6 sheet: 0.80 (0.24), residues: 460 loop : -0.75 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 415 TYR 0.012 0.001 TYR B 553 PHE 0.012 0.001 PHE A 417 TRP 0.008 0.001 TRP C 120 HIS 0.007 0.001 HIS B 532 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8242) covalent geometry : angle 0.65753 (11198) SS BOND : bond 0.00179 ( 17) SS BOND : angle 0.64467 ( 34) hydrogen bonds : bond 0.03209 ( 261) hydrogen bonds : angle 5.29373 ( 696) link_BETA1-4 : bond 0.01068 ( 8) link_BETA1-4 : angle 3.75838 ( 24) link_NAG-ASN : bond 0.00189 ( 12) link_NAG-ASN : angle 3.60198 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1879.72 seconds wall clock time: 33 minutes 15.65 seconds (1995.65 seconds total)