Starting phenix.real_space_refine on Mon Apr 28 22:19:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vse_43497/04_2025/8vse_43497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vse_43497/04_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_43497/04_2025/8vse_43497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vse_43497/04_2025/8vse_43497.map" model { file = "/net/cci-nas-00/data/ceres_data/8vse_43497/04_2025/8vse_43497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vse_43497/04_2025/8vse_43497.cif" } resolution = 3.8 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: 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.52, per 1000 atoms: 0.69 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: 2.54 Conformation dependent library (CDL) restraints added in 856.5 milliseconds 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: 1.03 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: 2.45 Time building geometry restraints manager: 2.84 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 574 or resid 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.780 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.180 ------------------------------------------------------------------------------- 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 : 8.67 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 (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: 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 TRP 0.005 0.001 TRP C 10 HIS 0.002 0.000 HIS B 500 PHE 0.006 0.001 PHE B 376 TYR 0.008 0.001 TYR B 424 ARG 0.001 0.000 ARG A 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 12) link_NAG-ASN : angle 3.09779 ( 36) link_BETA1-4 : bond 0.00922 ( 8) link_BETA1-4 : angle 3.37349 ( 24) hydrogen bonds : bond 0.08508 ( 261) hydrogen bonds : angle 4.72091 ( 696) SS BOND : bond 0.00141 ( 17) SS BOND : angle 0.52645 ( 34) covalent geometry : bond 0.00186 ( 8242) covalent geometry : angle 0.50880 (11198) *********************** 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 : 0.932 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: A 293 LEU cc_start: 0.5644 (OUTLIER) cc_final: 0.5434 (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: 0.6830 (m-40) REVERT: C 153 VAL cc_start: 0.7546 (t) cc_final: 0.7237 (p) REVERT: C 260 VAL cc_start: 0.8593 (t) cc_final: 0.8298 (p) REVERT: C 319 TYR cc_start: 0.7591 (m-80) cc_final: 0.7055 (m-80) outliers start: 13 outliers final: 4 residues processed: 158 average time/residue: 0.3162 time to fit residues: 61.7318 Evaluate side-chains 66 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 81 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 40.0000 chunk 24 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4050 r_free = 0.4050 target = 0.091556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.074094 restraints weight = 39600.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.076222 restraints weight = 22105.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.077634 restraints weight = 14828.776| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8279 Z= 0.217 Angle : 0.768 13.509 11292 Z= 0.373 Chirality : 0.046 0.313 1274 Planarity : 0.004 0.050 1432 Dihedral : 8.129 58.040 1463 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.28 % Allowed : 10.72 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.02 (0.28), residues: 955 helix: -0.49 (2.12), residues: 6 sheet: 1.59 (0.25), residues: 455 loop : -0.20 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 120 HIS 0.015 0.001 HIS B 532 PHE 0.016 0.002 PHE B 420 TYR 0.016 0.002 TYR C 174 ARG 0.008 0.001 ARG C 284 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 12) link_NAG-ASN : angle 3.64118 ( 36) link_BETA1-4 : bond 0.00603 ( 8) link_BETA1-4 : angle 3.28518 ( 24) hydrogen bonds : bond 0.03505 ( 261) hydrogen bonds : angle 4.83577 ( 696) SS BOND : bond 0.00791 ( 17) SS BOND : angle 2.07155 ( 34) covalent geometry : bond 0.00489 ( 8242) covalent geometry : angle 0.71880 (11198) *********************** 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 82 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7454 (tp) REVERT: A 389 SER cc_start: 0.8149 (m) cc_final: 0.7734 (p) REVERT: A 409 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8495 (p) REVERT: B 509 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7806 (mmm160) REVERT: B 559 TYR cc_start: 0.7820 (m-80) cc_final: 0.7525 (m-10) REVERT: C 260 VAL cc_start: 0.9030 (t) cc_final: 0.8778 (p) REVERT: C 320 ARG cc_start: 0.7250 (ttp80) cc_final: 0.7024 (ttp80) outliers start: 20 outliers final: 10 residues processed: 82 average time/residue: 0.2567 time to fit residues: 27.4893 Evaluate side-chains 59 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 244 LYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 75 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 91 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- 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** ** 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 = 0.4138 r_free = 0.4138 target = 0.095649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.077372 restraints weight = 47186.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.079135 restraints weight = 26775.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 74)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.080339 restraints weight = 18699.079| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8279 Z= 0.229 Angle : 0.748 13.410 11292 Z= 0.364 Chirality : 0.046 0.317 1274 Planarity : 0.004 0.051 1432 Dihedral : 8.270 59.482 1459 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.51 % Allowed : 11.86 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.59 (0.27), residues: 955 helix: -0.63 (2.04), residues: 6 sheet: 1.31 (0.24), residues: 449 loop : -0.47 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 487 HIS 0.006 0.001 HIS B 532 PHE 0.023 0.002 PHE B 420 TYR 0.020 0.002 TYR C 319 ARG 0.009 0.001 ARG C 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 12) link_NAG-ASN : angle 3.83034 ( 36) link_BETA1-4 : bond 0.00628 ( 8) link_BETA1-4 : angle 3.72408 ( 24) hydrogen bonds : bond 0.03730 ( 261) hydrogen bonds : angle 5.00124 ( 696) SS BOND : bond 0.00523 ( 17) SS BOND : angle 1.14410 ( 34) covalent geometry : bond 0.00499 ( 8242) covalent geometry : angle 0.69493 (11198) *********************** 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 74 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8654 (p) REVERT: B 327 GLU cc_start: 0.7628 (pm20) cc_final: 0.7367 (pm20) REVERT: B 509 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8099 (mmm160) REVERT: C 128 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6748 (t80) REVERT: C 170 GLN cc_start: 0.8343 (mp10) cc_final: 0.8079 (mp10) outliers start: 22 outliers final: 15 residues processed: 71 average time/residue: 0.2800 time to fit residues: 26.6304 Evaluate side-chains 61 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 509 ARG Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 104 MET 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 93 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 30.0000 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.096838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.078756 restraints weight = 46475.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.080590 restraints weight = 26189.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.081720 restraints weight = 18205.234| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3734 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= 0.140 Angle : 0.684 13.919 11292 Z= 0.328 Chirality : 0.045 0.309 1274 Planarity : 0.004 0.050 1432 Dihedral : 8.165 59.945 1459 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.08 % Allowed : 11.63 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.62 (0.28), residues: 955 helix: -0.48 (2.07), residues: 6 sheet: 1.26 (0.24), residues: 461 loop : -0.41 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 487 HIS 0.005 0.001 HIS A 568 PHE 0.010 0.001 PHE B 420 TYR 0.020 0.001 TYR C 174 ARG 0.008 0.001 ARG B 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 12) link_NAG-ASN : angle 3.62707 ( 36) link_BETA1-4 : bond 0.00842 ( 8) link_BETA1-4 : angle 3.71673 ( 24) hydrogen bonds : bond 0.03308 ( 261) hydrogen bonds : angle 4.98185 ( 696) SS BOND : bond 0.00239 ( 17) SS BOND : angle 0.88085 ( 34) covalent geometry : bond 0.00317 ( 8242) covalent geometry : angle 0.63011 (11198) *********************** 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 73 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 46 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8585 (p) REVERT: B 327 GLU cc_start: 0.7615 (pm20) cc_final: 0.7340 (pm20) REVERT: B 509 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8113 (mmm160) REVERT: B 559 TYR cc_start: 0.8042 (m-80) cc_final: 0.7580 (m-10) REVERT: C 124 ASP cc_start: 0.8273 (t70) cc_final: 0.8023 (t0) REVERT: C 128 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6474 (t80) REVERT: C 170 GLN cc_start: 0.8280 (mp10) cc_final: 0.7911 (mp10) outliers start: 27 outliers final: 12 residues processed: 70 average time/residue: 0.1909 time to fit residues: 19.0359 Evaluate side-chains 55 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 409 THR Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 104 MET 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 67 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 35 optimal weight: 30.0000 chunk 94 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4036 r_free = 0.4036 target = 0.089152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.072202 restraints weight = 39228.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.074125 restraints weight = 21514.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.075329 restraints weight = 14442.606| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8279 Z= 0.169 Angle : 0.685 13.889 11292 Z= 0.329 Chirality : 0.045 0.301 1274 Planarity : 0.004 0.050 1432 Dihedral : 8.182 58.593 1458 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.28 % Allowed : 12.09 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.43 (0.28), residues: 955 helix: -0.41 (2.05), residues: 6 sheet: 1.03 (0.24), residues: 469 loop : -0.46 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 487 HIS 0.003 0.001 HIS C 287 PHE 0.016 0.002 PHE A 420 TYR 0.014 0.001 TYR C 174 ARG 0.004 0.001 ARG C 284 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 12) link_NAG-ASN : angle 3.65900 ( 36) link_BETA1-4 : bond 0.00776 ( 8) link_BETA1-4 : angle 3.78333 ( 24) hydrogen bonds : bond 0.03439 ( 261) hydrogen bonds : angle 5.04770 ( 696) SS BOND : bond 0.00358 ( 17) SS BOND : angle 1.12919 ( 34) covalent geometry : bond 0.00379 ( 8242) covalent geometry : angle 0.62884 (11198) *********************** 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 65 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 CYS cc_start: 0.4890 (OUTLIER) cc_final: 0.4460 (p) REVERT: A 304 PHE cc_start: 0.6185 (m-80) cc_final: 0.5932 (m-10) REVERT: A 409 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8572 (p) REVERT: B 303 LYS cc_start: 0.6884 (mptt) cc_final: 0.6270 (mmtp) REVERT: B 448 LYS cc_start: 0.9077 (tppt) cc_final: 0.8812 (tppt) REVERT: B 509 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8191 (mmm-85) REVERT: C 128 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6531 (t80) REVERT: C 158 ASP cc_start: 0.8381 (p0) cc_final: 0.8086 (t0) REVERT: C 170 GLN cc_start: 0.8301 (mp10) cc_final: 0.8008 (mp10) outliers start: 20 outliers final: 12 residues processed: 63 average time/residue: 0.2255 time to fit residues: 19.7290 Evaluate side-chains 57 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 CYS 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 240 ASN 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 509 ARG Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 104 MET 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 37 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 44 optimal weight: 0.0870 chunk 67 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.087639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.070552 restraints weight = 39818.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.072469 restraints weight = 21789.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.073680 restraints weight = 14624.089| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4354 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= 0.211 Angle : 0.735 13.821 11292 Z= 0.357 Chirality : 0.045 0.292 1274 Planarity : 0.004 0.050 1432 Dihedral : 8.308 58.742 1458 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.19 % Allowed : 11.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.28), residues: 955 helix: -0.42 (2.00), residues: 6 sheet: 0.85 (0.24), residues: 461 loop : -0.50 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 487 HIS 0.004 0.001 HIS A 307 PHE 0.014 0.002 PHE B 420 TYR 0.012 0.002 TYR C 103 ARG 0.005 0.001 ARG C 284 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 12) link_NAG-ASN : angle 3.76669 ( 36) link_BETA1-4 : bond 0.00751 ( 8) link_BETA1-4 : angle 3.96049 ( 24) hydrogen bonds : bond 0.03713 ( 261) hydrogen bonds : angle 5.24278 ( 696) SS BOND : bond 0.00344 ( 17) SS BOND : angle 1.77677 ( 34) covalent geometry : bond 0.00462 ( 8242) covalent geometry : angle 0.67527 (11198) *********************** 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 70 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 42 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8704 (t) REVERT: B 448 LYS cc_start: 0.9132 (tppt) cc_final: 0.8821 (tppt) REVERT: B 509 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8203 (mmm-85) REVERT: C 128 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6523 (t80) REVERT: C 158 ASP cc_start: 0.8523 (p0) cc_final: 0.8098 (t0) REVERT: C 170 GLN cc_start: 0.8354 (mp10) cc_final: 0.8073 (mp10) outliers start: 28 outliers final: 14 residues processed: 68 average time/residue: 0.2199 time to fit residues: 20.8100 Evaluate side-chains 55 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 409 THR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 176 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 47 optimal weight: 0.0770 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 0.0770 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4011 r_free = 0.4011 target = 0.087420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.070513 restraints weight = 40829.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.072392 restraints weight = 22565.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.073601 restraints weight = 15290.924| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8279 Z= 0.189 Angle : 0.724 13.852 11292 Z= 0.348 Chirality : 0.045 0.284 1274 Planarity : 0.004 0.049 1432 Dihedral : 8.390 59.277 1458 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.39 % Allowed : 13.11 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.06 (0.28), residues: 955 helix: -0.49 (1.99), residues: 6 sheet: 0.66 (0.24), residues: 475 loop : -0.57 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 487 HIS 0.005 0.001 HIS A 568 PHE 0.012 0.002 PHE A 420 TYR 0.011 0.001 TYR A 548 ARG 0.002 0.001 ARG B 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 12) link_NAG-ASN : angle 3.70232 ( 36) link_BETA1-4 : bond 0.00840 ( 8) link_BETA1-4 : angle 3.99773 ( 24) hydrogen bonds : bond 0.03518 ( 261) hydrogen bonds : angle 5.32676 ( 696) SS BOND : bond 0.00282 ( 17) SS BOND : angle 1.46711 ( 34) covalent geometry : bond 0.00415 ( 8242) covalent geometry : angle 0.66562 (11198) *********************** 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 64 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8567 (tm-30) REVERT: B 509 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8149 (mmm160) REVERT: C 128 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6474 (t80) REVERT: C 146 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8364 (tp40) REVERT: C 147 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8307 (m-40) REVERT: C 158 ASP cc_start: 0.8348 (p0) cc_final: 0.7986 (t0) REVERT: C 170 GLN cc_start: 0.8294 (mp10) cc_final: 0.8063 (mp10) outliers start: 21 outliers final: 13 residues processed: 62 average time/residue: 0.2160 time to fit residues: 18.7708 Evaluate side-chains 58 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 CYS 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 244 LYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 147 ASN 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 46 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 92 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.088267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.071382 restraints weight = 39835.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.073328 restraints weight = 21484.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.074562 restraints weight = 14341.532| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4592 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= 0.134 Angle : 0.713 13.991 11292 Z= 0.339 Chirality : 0.046 0.320 1274 Planarity : 0.004 0.048 1432 Dihedral : 8.323 59.068 1458 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.94 % Allowed : 14.25 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.10 (0.28), residues: 955 helix: -0.46 (2.01), residues: 6 sheet: 0.67 (0.24), residues: 475 loop : -0.52 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 120 HIS 0.004 0.001 HIS C 287 PHE 0.018 0.002 PHE B 537 TYR 0.014 0.001 TYR B 548 ARG 0.006 0.001 ARG C 284 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 12) link_NAG-ASN : angle 3.60875 ( 36) link_BETA1-4 : bond 0.00964 ( 8) link_BETA1-4 : angle 3.89138 ( 24) hydrogen bonds : bond 0.03200 ( 261) hydrogen bonds : angle 5.21443 ( 696) SS BOND : bond 0.00183 ( 17) SS BOND : angle 1.49892 ( 34) covalent geometry : bond 0.00298 ( 8242) covalent geometry : angle 0.65658 (11198) *********************** 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 58 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 509 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8134 (mmm-85) REVERT: C 128 PHE cc_start: 0.7075 (OUTLIER) cc_final: 0.6361 (t80) REVERT: C 158 ASP cc_start: 0.8380 (p0) cc_final: 0.8063 (t0) REVERT: C 170 GLN cc_start: 0.8239 (mp10) cc_final: 0.8011 (mp10) outliers start: 17 outliers final: 12 residues processed: 57 average time/residue: 0.2076 time to fit residues: 16.9289 Evaluate side-chains 52 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 CYS 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 368 GLU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 509 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 44 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 ** 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 = 0.4008 r_free = 0.4008 target = 0.087222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.070363 restraints weight = 41588.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.072225 restraints weight = 22963.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.073441 restraints weight = 15517.054| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8279 Z= 0.179 Angle : 0.727 13.801 11292 Z= 0.348 Chirality : 0.045 0.286 1274 Planarity : 0.004 0.048 1432 Dihedral : 8.381 59.803 1458 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.82 % Allowed : 14.94 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.02 (0.28), residues: 955 helix: -0.50 (1.96), residues: 6 sheet: 0.72 (0.24), residues: 463 loop : -0.67 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 487 HIS 0.004 0.001 HIS C 287 PHE 0.018 0.002 PHE C 101 TYR 0.022 0.001 TYR B 548 ARG 0.004 0.001 ARG C 284 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 12) link_NAG-ASN : angle 3.68508 ( 36) link_BETA1-4 : bond 0.00886 ( 8) link_BETA1-4 : angle 3.89298 ( 24) hydrogen bonds : bond 0.03440 ( 261) hydrogen bonds : angle 5.30323 ( 696) SS BOND : bond 0.00262 ( 17) SS BOND : angle 1.52706 ( 34) covalent geometry : bond 0.00399 ( 8242) covalent geometry : angle 0.67112 (11198) *********************** 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 56 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 509 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8139 (mmm-85) REVERT: C 128 PHE cc_start: 0.7195 (OUTLIER) cc_final: 0.6509 (t80) REVERT: C 158 ASP cc_start: 0.8398 (p0) cc_final: 0.8012 (t0) REVERT: C 170 GLN cc_start: 0.8300 (mp10) cc_final: 0.8078 (mp10) outliers start: 16 outliers final: 13 residues processed: 56 average time/residue: 0.2309 time to fit residues: 18.5159 Evaluate side-chains 54 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 CYS 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 244 LYS Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 509 ARG 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 25 optimal weight: 3.9990 chunk 2 optimal weight: 0.0050 chunk 33 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.088241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.071295 restraints weight = 40284.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.073176 restraints weight = 21882.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.074402 restraints weight = 14653.118| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8279 Z= 0.126 Angle : 0.701 14.029 11292 Z= 0.333 Chirality : 0.045 0.283 1274 Planarity : 0.004 0.047 1432 Dihedral : 8.301 58.963 1458 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.48 % Allowed : 15.85 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.10 (0.28), residues: 955 helix: 0.70 (2.01), residues: 7 sheet: 0.72 (0.25), residues: 469 loop : -0.58 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 487 HIS 0.004 0.001 HIS C 287 PHE 0.018 0.002 PHE C 155 TYR 0.011 0.001 TYR B 548 ARG 0.007 0.001 ARG C 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 12) link_NAG-ASN : angle 3.55281 ( 36) link_BETA1-4 : bond 0.01011 ( 8) link_BETA1-4 : angle 3.80997 ( 24) hydrogen bonds : bond 0.03053 ( 261) hydrogen bonds : angle 5.23642 ( 696) SS BOND : bond 0.00177 ( 17) SS BOND : angle 1.43488 ( 34) covalent geometry : bond 0.00285 ( 8242) covalent geometry : angle 0.64586 (11198) ********************** 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 55 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 MET cc_start: 0.7167 (tpp) cc_final: 0.6728 (tpp) REVERT: B 509 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8208 (mmm-85) REVERT: C 128 PHE cc_start: 0.7066 (OUTLIER) cc_final: 0.6376 (t80) REVERT: C 158 ASP cc_start: 0.8377 (p0) cc_final: 0.8004 (t0) REVERT: C 170 GLN cc_start: 0.8224 (mp10) cc_final: 0.8018 (mp10) REVERT: C 320 ARG cc_start: 0.7359 (ttp-110) cc_final: 0.7111 (ttm170) outliers start: 13 outliers final: 11 residues processed: 55 average time/residue: 0.2738 time to fit residues: 20.6330 Evaluate side-chains 53 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 CYS 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 368 GLU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 509 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 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 = 0.4035 r_free = 0.4035 target = 0.088527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.071649 restraints weight = 40852.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.073506 restraints weight = 22549.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.074690 restraints weight = 15229.262| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4753 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= 0.123 Angle : 0.696 13.922 11292 Z= 0.330 Chirality : 0.045 0.291 1274 Planarity : 0.004 0.047 1432 Dihedral : 8.249 59.243 1458 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.71 % Allowed : 15.51 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.16 (0.28), residues: 955 helix: 0.75 (2.03), residues: 7 sheet: 0.83 (0.25), residues: 459 loop : -0.60 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 487 HIS 0.003 0.001 HIS C 287 PHE 0.019 0.001 PHE C 155 TYR 0.010 0.001 TYR C 103 ARG 0.014 0.001 ARG A 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 12) link_NAG-ASN : angle 3.53964 ( 36) link_BETA1-4 : bond 0.00989 ( 8) link_BETA1-4 : angle 3.70590 ( 24) hydrogen bonds : bond 0.02986 ( 261) hydrogen bonds : angle 5.20031 ( 696) SS BOND : bond 0.00178 ( 17) SS BOND : angle 1.38397 ( 34) covalent geometry : bond 0.00281 ( 8242) covalent geometry : angle 0.64297 (11198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3283.66 seconds wall clock time: 57 minutes 39.30 seconds (3459.30 seconds total)