Starting phenix.real_space_refine on Sun May 11 14:03:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vse_43497/05_2025/8vse_43497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vse_43497/05_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_43497/05_2025/8vse_43497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vse_43497/05_2025/8vse_43497.map" model { file = "/net/cci-nas-00/data/ceres_data/8vse_43497/05_2025/8vse_43497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vse_43497/05_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-5687/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: 5.12, per 1000 atoms: 0.64 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: 2.21 Conformation dependent library (CDL) restraints added in 969.7 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: 1.08 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: 2.44 Time building geometry restraints manager: 2.59 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: 1.360 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.180 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.940 ------------------------------------------------------------------------------- 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 : 0.927 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: 0.2951 time to fit residues: 57.6531 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 : 0.987 ------------------------------------------------------------------------------- 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 = 0.091557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.074102 restraints weight = 39600.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.076242 restraints weight = 22093.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.077620 restraints weight = 14796.181| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 3.64117 ( 36) link_BETA1-4 : bond 0.00603 ( 8) link_BETA1-4 : angle 3.28516 ( 24) hydrogen bonds : bond 0.03505 ( 261) hydrogen bonds : angle 4.83578 ( 696) SS BOND : bond 0.00792 ( 17) SS BOND : angle 2.07153 ( 34) covalent geometry : bond 0.00489 ( 8242) covalent geometry : angle 0.71879 (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 : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7470 (tp) REVERT: A 389 SER cc_start: 0.8150 (m) cc_final: 0.7734 (p) REVERT: A 409 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8492 (p) REVERT: B 509 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7804 (mmm160) REVERT: B 559 TYR cc_start: 0.7813 (m-80) cc_final: 0.7521 (m-10) REVERT: C 260 VAL cc_start: 0.9018 (t) cc_final: 0.8766 (p) REVERT: C 320 ARG cc_start: 0.7237 (ttp80) cc_final: 0.7013 (ttp80) outliers start: 20 outliers final: 10 residues processed: 82 average time/residue: 0.2623 time to fit residues: 28.1208 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 : 0.922 ------------------------------------------------------------------------------- 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: 0.9980 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 91 optimal weight: 0.0270 chunk 0 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.096146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.078036 restraints weight = 47186.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.079813 restraints weight = 26715.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.080774 restraints weight = 18651.159| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8279 Z= 0.208 Angle : 0.730 13.488 11292 Z= 0.354 Chirality : 0.046 0.315 1274 Planarity : 0.004 0.052 1432 Dihedral : 8.207 59.806 1459 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % 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: 0.67 (0.28), residues: 955 helix: -0.60 (2.06), residues: 6 sheet: 1.39 (0.24), residues: 448 loop : -0.45 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 487 HIS 0.006 0.001 HIS B 532 PHE 0.021 0.002 PHE B 420 TYR 0.017 0.002 TYR C 319 ARG 0.008 0.001 ARG C 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 12) link_NAG-ASN : angle 3.73192 ( 36) link_BETA1-4 : bond 0.00711 ( 8) link_BETA1-4 : angle 3.66703 ( 24) hydrogen bonds : bond 0.03593 ( 261) hydrogen bonds : angle 4.93430 ( 696) SS BOND : bond 0.00387 ( 17) SS BOND : angle 1.10309 ( 34) covalent geometry : bond 0.00459 ( 8242) covalent geometry : angle 0.67823 (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 75 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8649 (p) REVERT: B 327 GLU cc_start: 0.7613 (pm20) cc_final: 0.7343 (pm20) REVERT: B 509 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8109 (mmm160) REVERT: C 128 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6692 (t80) REVERT: C 170 GLN cc_start: 0.8334 (mp10) cc_final: 0.8063 (mp10) outliers start: 22 outliers final: 15 residues processed: 72 average time/residue: 0.2579 time to fit residues: 24.5951 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 : 0.920 ------------------------------------------------------------------------------- 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: 1.9990 chunk 79 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 0.0040 chunk 40 optimal weight: 30.0000 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.9394 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.090350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.073393 restraints weight = 39640.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.075347 restraints weight = 21594.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.076571 restraints weight = 14375.000| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8279 Z= 0.144 Angle : 0.677 13.904 11292 Z= 0.325 Chirality : 0.045 0.312 1274 Planarity : 0.004 0.050 1432 Dihedral : 8.137 59.969 1459 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.08 % Allowed : 11.74 % Favored : 85.18 % 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: 0.65 (0.28), residues: 955 helix: -0.48 (2.08), residues: 6 sheet: 1.27 (0.24), residues: 461 loop : -0.38 (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 0.019 0.001 TYR C 174 ARG 0.004 0.001 ARG C 284 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 12) link_NAG-ASN : angle 3.62687 ( 36) link_BETA1-4 : bond 0.00816 ( 8) link_BETA1-4 : angle 3.70020 ( 24) hydrogen bonds : bond 0.03298 ( 261) hydrogen bonds : angle 4.94474 ( 696) SS BOND : bond 0.00252 ( 17) SS BOND : angle 0.87819 ( 34) covalent geometry : bond 0.00328 ( 8242) covalent geometry : angle 0.62335 (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 74 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.6240 (m-80) cc_final: 0.6001 (m-10) REVERT: A 409 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8519 (p) REVERT: A 493 MET cc_start: 0.3555 (ttt) cc_final: 0.3311 (ttt) REVERT: B 559 TYR cc_start: 0.7884 (m-80) cc_final: 0.7513 (m-10) REVERT: C 124 ASP cc_start: 0.8157 (t70) cc_final: 0.7948 (t0) REVERT: C 128 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6491 (t80) REVERT: C 170 GLN cc_start: 0.8189 (mp10) cc_final: 0.7832 (mp10) outliers start: 27 outliers final: 12 residues processed: 71 average time/residue: 0.2002 time to fit residues: 20.0760 Evaluate side-chains 54 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 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 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: 8.9990 chunk 59 optimal weight: 0.9980 chunk 35 optimal weight: 30.0000 chunk 94 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.087335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.070011 restraints weight = 40254.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.071891 restraints weight = 22081.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.073089 restraints weight = 14936.838| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8279 Z= 0.254 Angle : 0.763 13.843 11292 Z= 0.371 Chirality : 0.046 0.289 1274 Planarity : 0.005 0.051 1432 Dihedral : 8.388 59.607 1458 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.18 % Favored : 93.72 % Rotamer: Outliers : 2.51 % Allowed : 12.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 955 helix: -2.83 (1.19), residues: 12 sheet: 0.84 (0.24), residues: 457 loop : -0.61 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 487 HIS 0.005 0.001 HIS A 307 PHE 0.018 0.002 PHE B 420 TYR 0.014 0.002 TYR A 548 ARG 0.005 0.001 ARG B 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 12) link_NAG-ASN : angle 3.92919 ( 36) link_BETA1-4 : bond 0.00613 ( 8) link_BETA1-4 : angle 4.01734 ( 24) hydrogen bonds : bond 0.04022 ( 261) hydrogen bonds : angle 5.22824 ( 696) SS BOND : bond 0.00536 ( 17) SS BOND : angle 1.27898 ( 34) covalent geometry : bond 0.00551 ( 8242) covalent geometry : angle 0.70509 (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: 22 poor density : 43 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8729 (t) REVERT: A 498 SER cc_start: 0.5947 (OUTLIER) cc_final: 0.5377 (t) REVERT: B 448 LYS cc_start: 0.9144 (tppt) cc_final: 0.8831 (tppt) REVERT: C 128 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6672 (t80) REVERT: C 158 ASP cc_start: 0.8481 (p0) cc_final: 0.8078 (t0) REVERT: C 170 GLN cc_start: 0.8371 (mp10) cc_final: 0.8098 (mp10) REVERT: C 176 VAL cc_start: 0.8865 (t) cc_final: 0.8594 (m) outliers start: 22 outliers final: 13 residues processed: 63 average time/residue: 0.1813 time to fit residues: 16.6142 Evaluate side-chains 55 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 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 81 VAL 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: 4.9990 chunk 20 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** C 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.086567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.069393 restraints weight = 39724.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.071292 restraints weight = 21796.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.072490 restraints weight = 14711.059| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8279 Z= 0.235 Angle : 0.753 13.870 11292 Z= 0.366 Chirality : 0.046 0.282 1274 Planarity : 0.005 0.051 1432 Dihedral : 8.532 59.399 1458 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.28 % Allowed : 13.45 % Favored : 84.26 % 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: -0.08 (0.27), residues: 955 helix: -0.60 (1.95), residues: 6 sheet: 0.62 (0.24), residues: 455 loop : -0.67 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 120 HIS 0.008 0.001 HIS A 568 PHE 0.015 0.002 PHE A 376 TYR 0.014 0.002 TYR A 548 ARG 0.006 0.001 ARG C 284 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 12) link_NAG-ASN : angle 3.84562 ( 36) link_BETA1-4 : bond 0.00826 ( 8) link_BETA1-4 : angle 4.12023 ( 24) hydrogen bonds : bond 0.03887 ( 261) hydrogen bonds : angle 5.43402 ( 696) SS BOND : bond 0.00353 ( 17) SS BOND : angle 1.15045 ( 34) covalent geometry : bond 0.00517 ( 8242) covalent geometry : angle 0.69602 (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 64 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8728 (t) REVERT: B 448 LYS cc_start: 0.9191 (tppt) cc_final: 0.8822 (tppt) REVERT: C 128 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.6591 (t80) REVERT: C 158 ASP cc_start: 0.8509 (p0) cc_final: 0.8066 (t0) REVERT: C 170 GLN cc_start: 0.8427 (mp10) cc_final: 0.8168 (mp10) outliers start: 20 outliers final: 13 residues processed: 62 average time/residue: 0.1819 time to fit residues: 16.3196 Evaluate side-chains 58 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 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 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=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: 0.9980 chunk 93 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 19 optimal weight: 0.0060 chunk 80 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.086740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.069650 restraints weight = 38871.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.071564 restraints weight = 21047.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.072767 restraints weight = 14062.477| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8279 Z= 0.189 Angle : 0.726 13.980 11292 Z= 0.348 Chirality : 0.045 0.279 1274 Planarity : 0.004 0.050 1432 Dihedral : 8.527 59.521 1458 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.05 % Allowed : 14.14 % 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: -0.15 (0.27), residues: 955 helix: -0.60 (1.93), residues: 6 sheet: 0.55 (0.24), residues: 455 loop : -0.69 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 487 HIS 0.004 0.001 HIS B 532 PHE 0.017 0.002 PHE B 537 TYR 0.012 0.001 TYR A 548 ARG 0.003 0.001 ARG B 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 12) link_NAG-ASN : angle 3.79230 ( 36) link_BETA1-4 : bond 0.00891 ( 8) link_BETA1-4 : angle 3.98353 ( 24) hydrogen bonds : bond 0.03650 ( 261) hydrogen bonds : angle 5.46806 ( 696) SS BOND : bond 0.00251 ( 17) SS BOND : angle 0.95775 ( 34) covalent geometry : bond 0.00414 ( 8242) covalent geometry : angle 0.66994 (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 62 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8565 (tm-30) REVERT: A 409 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8731 (t) REVERT: C 128 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6539 (t80) REVERT: C 158 ASP cc_start: 0.8581 (p0) cc_final: 0.8056 (t0) REVERT: C 170 GLN cc_start: 0.8429 (mp10) cc_final: 0.8162 (mp10) REVERT: C 176 VAL cc_start: 0.8746 (t) cc_final: 0.8309 (m) outliers start: 18 outliers final: 14 residues processed: 60 average time/residue: 0.1983 time to fit residues: 17.1397 Evaluate side-chains 57 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 A residue 409 THR 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 104 MET Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 149 ILE 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: 1.9990 chunk 78 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.087308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.070140 restraints weight = 39814.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.072013 restraints weight = 22227.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.073230 restraints weight = 15138.257| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8279 Z= 0.134 Angle : 0.692 14.005 11292 Z= 0.329 Chirality : 0.046 0.286 1274 Planarity : 0.004 0.049 1432 Dihedral : 8.401 58.434 1458 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.82 % Allowed : 14.82 % Favored : 83.35 % 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: 0.57 (1.99), residues: 7 sheet: 0.67 (0.24), residues: 469 loop : -0.64 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 487 HIS 0.004 0.001 HIS C 287 PHE 0.017 0.002 PHE C 155 TYR 0.013 0.001 TYR B 548 ARG 0.007 0.001 ARG C 284 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 12) link_NAG-ASN : angle 3.64632 ( 36) link_BETA1-4 : bond 0.01015 ( 8) link_BETA1-4 : angle 3.87032 ( 24) hydrogen bonds : bond 0.03190 ( 261) hydrogen bonds : angle 5.35194 ( 696) SS BOND : bond 0.00194 ( 17) SS BOND : angle 0.83614 ( 34) covalent geometry : bond 0.00303 ( 8242) covalent geometry : angle 0.63746 (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 57 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8566 (tm-30) REVERT: C 128 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6327 (t80) REVERT: C 158 ASP cc_start: 0.8469 (p0) cc_final: 0.8072 (t0) REVERT: C 176 VAL cc_start: 0.8769 (t) cc_final: 0.8416 (m) outliers start: 16 outliers final: 10 residues processed: 57 average time/residue: 0.1869 time to fit residues: 15.5745 Evaluate side-chains 52 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 321 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 0.4980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.086708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.069603 restraints weight = 41114.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.071502 restraints weight = 22403.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.072726 restraints weight = 15033.623| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4928 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= 0.189 Angle : 0.732 13.944 11292 Z= 0.352 Chirality : 0.045 0.286 1274 Planarity : 0.004 0.049 1432 Dihedral : 8.530 59.968 1458 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.71 % Allowed : 15.17 % Favored : 83.12 % 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: -0.21 (0.27), residues: 955 helix: 0.52 (1.95), residues: 7 sheet: 0.56 (0.24), residues: 451 loop : -0.80 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 120 HIS 0.012 0.001 HIS B 532 PHE 0.014 0.002 PHE B 376 TYR 0.023 0.001 TYR B 548 ARG 0.006 0.001 ARG C 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 12) link_NAG-ASN : angle 3.76202 ( 36) link_BETA1-4 : bond 0.00905 ( 8) link_BETA1-4 : angle 3.83726 ( 24) hydrogen bonds : bond 0.03601 ( 261) hydrogen bonds : angle 5.44582 ( 696) SS BOND : bond 0.00274 ( 17) SS BOND : angle 0.93686 ( 34) covalent geometry : bond 0.00419 ( 8242) covalent geometry : angle 0.67851 (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: 15 poor density : 41 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8573 (tm-30) REVERT: C 128 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6555 (t80) REVERT: C 158 ASP cc_start: 0.8459 (p0) cc_final: 0.7989 (t70) REVERT: C 176 VAL cc_start: 0.8728 (t) cc_final: 0.8266 (m) REVERT: C 320 ARG cc_start: 0.7536 (ttp-110) cc_final: 0.7030 (ttm170) outliers start: 15 outliers final: 11 residues processed: 56 average time/residue: 0.1880 time to fit residues: 15.5357 Evaluate side-chains 51 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 25 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 81 optimal weight: 0.0980 chunk 7 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 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 = 0.3979 r_free = 0.3979 target = 0.085994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.068897 restraints weight = 40487.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.070776 restraints weight = 22274.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.071939 restraints weight = 15087.681| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8279 Z= 0.207 Angle : 0.752 13.900 11292 Z= 0.364 Chirality : 0.046 0.272 1274 Planarity : 0.004 0.049 1432 Dihedral : 8.731 59.551 1458 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % 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: -0.31 (0.28), residues: 955 helix: 0.49 (1.91), residues: 7 sheet: 0.47 (0.24), residues: 451 loop : -0.85 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 10 HIS 0.013 0.001 HIS B 532 PHE 0.016 0.002 PHE B 376 TYR 0.014 0.002 TYR B 548 ARG 0.005 0.001 ARG C 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 12) link_NAG-ASN : angle 3.79964 ( 36) link_BETA1-4 : bond 0.00918 ( 8) link_BETA1-4 : angle 3.77760 ( 24) hydrogen bonds : bond 0.03737 ( 261) hydrogen bonds : angle 5.56151 ( 696) SS BOND : bond 0.00266 ( 17) SS BOND : angle 0.95588 ( 34) covalent geometry : bond 0.00453 ( 8242) covalent geometry : angle 0.69997 (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 53 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8565 (tm-30) REVERT: A 427 GLU cc_start: 0.7588 (pm20) cc_final: 0.7371 (pm20) REVERT: C 100 VAL cc_start: 0.9171 (t) cc_final: 0.8956 (m) REVERT: C 128 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.6611 (t80) REVERT: C 158 ASP cc_start: 0.8561 (p0) cc_final: 0.7977 (t0) REVERT: C 176 VAL cc_start: 0.8765 (t) cc_final: 0.8294 (m) outliers start: 15 outliers final: 12 residues processed: 52 average time/residue: 0.1962 time to fit residues: 15.1078 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 : 0.877 ------------------------------------------------------------------------------- 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 149 ILE 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 38 optimal weight: 0.1980 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 61 optimal weight: 0.0980 chunk 80 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 56 optimal weight: 0.0770 chunk 35 optimal weight: 10.0000 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.088791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.072050 restraints weight = 40982.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.073927 restraints weight = 22514.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.075145 restraints weight = 15239.996| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8279 Z= 0.116 Angle : 0.703 14.355 11292 Z= 0.335 Chirality : 0.046 0.280 1274 Planarity : 0.004 0.070 1432 Dihedral : 8.417 59.495 1458 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.48 % Allowed : 15.39 % Favored : 83.12 % 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: -0.07 (0.28), residues: 955 helix: 0.90 (2.08), residues: 7 sheet: 0.66 (0.25), residues: 466 loop : -0.76 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 120 HIS 0.008 0.001 HIS B 532 PHE 0.023 0.002 PHE C 155 TYR 0.014 0.001 TYR C 174 ARG 0.008 0.001 ARG C 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 12) link_NAG-ASN : angle 3.55146 ( 36) link_BETA1-4 : bond 0.01101 ( 8) link_BETA1-4 : angle 3.69718 ( 24) hydrogen bonds : bond 0.03023 ( 261) hydrogen bonds : angle 5.37481 ( 696) SS BOND : bond 0.00130 ( 17) SS BOND : angle 0.87225 ( 34) covalent geometry : bond 0.00264 ( 8242) covalent geometry : angle 0.65330 (11198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3061.90 seconds wall clock time: 54 minutes 21.11 seconds (3261.11 seconds total)