Starting phenix.real_space_refine on Wed Jan 15 06:56:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vse_43497/01_2025/8vse_43497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vse_43497/01_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_43497/01_2025/8vse_43497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vse_43497/01_2025/8vse_43497.map" model { file = "/net/cci-nas-00/data/ceres_data/8vse_43497/01_2025/8vse_43497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vse_43497/01_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-5571/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: 5.39, per 1000 atoms: 0.67 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: 2.23 Conformation dependent library (CDL) restraints added in 863.3 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: 1.21 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: 2.55 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.020 Find NCS groups from input model: 0.280 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.570 ------------------------------------------------------------------------------- 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 8242 Z= 0.113 Angle : 0.509 9.602 11198 Z= 0.253 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 *********************** 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 : 0.961 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: 0.3230 time to fit residues: 63.5273 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 : 0.869 ------------------------------------------------------------------------------- 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 8242 Z= 0.321 Angle : 0.719 11.658 11198 Z= 0.360 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 *********************** 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 : 0.948 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: 0.2648 time to fit residues: 28.3207 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 : 0.916 ------------------------------------------------------------------------------- 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: 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: 1.8046 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.096187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.077995 restraints weight = 47167.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.079797 restraints weight = 26744.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.080852 restraints weight = 18630.937| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8242 Z= 0.293 Angle : 0.676 9.607 11198 Z= 0.341 Chirality : 0.046 0.316 1274 Planarity : 0.004 0.051 1432 Dihedral : 8.200 59.871 1459 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.51 % Allowed : 11.97 % Favored : 85.52 % 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: -0.59 (2.07), residues: 6 sheet: 1.38 (0.24), residues: 448 loop : -0.46 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 487 HIS 0.007 0.001 HIS B 532 PHE 0.021 0.002 PHE B 420 TYR 0.021 0.002 TYR C 319 ARG 0.008 0.001 ARG C 38 *********************** 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 : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8651 (p) REVERT: B 327 GLU cc_start: 0.7609 (pm20) cc_final: 0.7342 (pm20) REVERT: B 509 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8113 (mmm160) REVERT: C 128 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6716 (t80) REVERT: C 170 GLN cc_start: 0.8313 (mp10) cc_final: 0.8049 (mp10) outliers start: 22 outliers final: 16 residues processed: 71 average time/residue: 0.2489 time to fit residues: 23.9335 Evaluate side-chains 63 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 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 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 103 TYR 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: 0.9980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 30.0000 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.096003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.079823 restraints weight = 46578.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.080744 restraints weight = 26182.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.081308 restraints weight = 20121.061| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8242 Z= 0.250 Angle : 0.637 9.713 11198 Z= 0.322 Chirality : 0.045 0.308 1274 Planarity : 0.004 0.051 1432 Dihedral : 8.175 58.897 1459 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.74 % Allowed : 11.74 % Favored : 85.52 % 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: 0.56 (0.28), residues: 955 helix: -0.50 (2.05), residues: 6 sheet: 1.25 (0.24), residues: 450 loop : -0.45 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 487 HIS 0.006 0.001 HIS A 361 PHE 0.013 0.001 PHE B 420 TYR 0.020 0.001 TYR C 174 ARG 0.005 0.001 ARG C 284 *********************** 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 71 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 47 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8655 (p) REVERT: B 327 GLU cc_start: 0.7627 (pm20) cc_final: 0.7349 (pm20) REVERT: B 509 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8173 (mmm160) REVERT: B 559 TYR cc_start: 0.8076 (m-80) cc_final: 0.7624 (m-10) REVERT: C 124 ASP cc_start: 0.8318 (t70) cc_final: 0.8055 (t0) REVERT: C 128 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6488 (t80) REVERT: C 158 ASP cc_start: 0.8518 (p0) cc_final: 0.8302 (t0) REVERT: C 170 GLN cc_start: 0.8309 (mp10) cc_final: 0.7943 (mp10) outliers start: 24 outliers final: 12 residues processed: 67 average time/residue: 0.2291 time to fit residues: 20.9692 Evaluate side-chains 59 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 B residue 509 ARG 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: 0.9990 chunk 93 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 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: 0.8980 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.088808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.071920 restraints weight = 39292.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.073810 restraints weight = 21498.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.074994 restraints weight = 14405.890| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8242 Z= 0.245 Angle : 0.628 9.710 11198 Z= 0.317 Chirality : 0.045 0.297 1274 Planarity : 0.004 0.050 1432 Dihedral : 8.203 58.259 1458 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.86 % Favored : 94.03 % Rotamer: Outliers : 2.28 % Allowed : 12.20 % Favored : 85.52 % 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: 0.33 (0.28), residues: 955 helix: -0.41 (2.05), residues: 6 sheet: 1.01 (0.24), residues: 454 loop : -0.53 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 487 HIS 0.003 0.001 HIS C 287 PHE 0.016 0.002 PHE A 420 TYR 0.013 0.001 TYR C 174 ARG 0.004 0.001 ARG C 284 *********************** 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 68 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8577 (p) REVERT: B 327 GLU cc_start: 0.7525 (pm20) cc_final: 0.7315 (pm20) REVERT: B 448 LYS cc_start: 0.9094 (tppt) cc_final: 0.8819 (tppt) REVERT: B 509 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8187 (mmm-85) REVERT: C 124 ASP cc_start: 0.8245 (t70) cc_final: 0.7921 (t0) REVERT: C 128 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6535 (t80) REVERT: C 170 GLN cc_start: 0.8308 (mp10) cc_final: 0.8024 (mp10) outliers start: 20 outliers final: 12 residues processed: 67 average time/residue: 0.2221 time to fit residues: 20.4549 Evaluate side-chains 57 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 B residue 509 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 37 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 67 optimal weight: 0.0980 chunk 89 optimal weight: 8.9990 chunk 45 optimal weight: 0.0010 chunk 66 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.9390 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.087483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.070460 restraints weight = 40089.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.072364 restraints weight = 22045.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.073541 restraints weight = 14860.775| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8242 Z= 0.310 Angle : 0.671 9.621 11198 Z= 0.340 Chirality : 0.045 0.290 1274 Planarity : 0.004 0.050 1432 Dihedral : 8.285 58.917 1458 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.28 % Allowed : 12.66 % Favored : 85.06 % 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: 0.17 (0.27), residues: 955 helix: -0.40 (2.00), residues: 6 sheet: 0.87 (0.24), residues: 444 loop : -0.57 (0.28), residues: 505 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 0.014 0.002 PHE B 420 TYR 0.012 0.002 TYR A 548 ARG 0.005 0.001 ARG C 284 *********************** 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 : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8746 (t) REVERT: B 327 GLU cc_start: 0.7632 (pm20) cc_final: 0.7386 (pm20) REVERT: B 448 LYS cc_start: 0.9149 (tppt) cc_final: 0.8835 (tppt) REVERT: B 509 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8162 (mmm160) REVERT: C 128 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6553 (t80) REVERT: C 170 GLN cc_start: 0.8358 (mp10) cc_final: 0.8064 (mp10) outliers start: 20 outliers final: 11 residues processed: 63 average time/residue: 0.2247 time to fit residues: 19.8346 Evaluate side-chains 53 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 93 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 19 optimal weight: 0.0670 chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 overall best weight: 1.5122 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.087462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.070472 restraints weight = 39659.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.072367 restraints weight = 21560.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.073583 restraints weight = 14405.994| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8242 Z= 0.253 Angle : 0.640 9.564 11198 Z= 0.323 Chirality : 0.045 0.284 1274 Planarity : 0.004 0.049 1432 Dihedral : 8.282 59.190 1458 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.94 % Allowed : 13.57 % 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: 0.11 (0.27), residues: 955 helix: -0.34 (2.03), residues: 6 sheet: 0.74 (0.24), residues: 452 loop : -0.52 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 487 HIS 0.005 0.001 HIS B 532 PHE 0.012 0.002 PHE C 155 TYR 0.012 0.001 TYR C 103 ARG 0.003 0.001 ARG B 504 *********************** 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 59 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8560 (tm-30) REVERT: A 409 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8736 (t) REVERT: B 327 GLU cc_start: 0.7626 (pm20) cc_final: 0.7409 (pm20) REVERT: B 509 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8145 (mmm160) REVERT: C 128 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6457 (t80) REVERT: C 158 ASP cc_start: 0.8523 (p0) cc_final: 0.8177 (t0) REVERT: C 170 GLN cc_start: 0.8397 (mp10) cc_final: 0.8136 (mp10) REVERT: C 320 ARG cc_start: 0.7298 (ttp80) cc_final: 0.7073 (ttp-110) outliers start: 17 outliers final: 12 residues processed: 57 average time/residue: 0.2299 time to fit residues: 18.1696 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 : 0.960 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- 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: 0.9980 chunk 35 optimal weight: 30.0000 chunk 32 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 84 optimal weight: 0.0770 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.0570 chunk 92 optimal weight: 0.9980 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.089339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.072612 restraints weight = 41031.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.074513 restraints weight = 22514.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.075690 restraints weight = 15113.071| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8242 Z= 0.170 Angle : 0.612 9.557 11198 Z= 0.305 Chirality : 0.045 0.292 1274 Planarity : 0.004 0.048 1432 Dihedral : 8.138 58.431 1458 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.37 % Allowed : 14.37 % 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: 0.30 (0.28), residues: 955 helix: -0.39 (2.06), residues: 6 sheet: 0.84 (0.24), residues: 470 loop : -0.42 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 120 HIS 0.005 0.001 HIS A 500 PHE 0.017 0.001 PHE C 155 TYR 0.014 0.001 TYR C 283 ARG 0.009 0.001 ARG C 284 *********************** 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 55 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 509 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8110 (mmm-85) REVERT: B 559 TYR cc_start: 0.7871 (m-80) cc_final: 0.7477 (m-10) REVERT: C 104 MET cc_start: 0.7306 (pmm) cc_final: 0.6466 (tpt) REVERT: C 128 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.6164 (t80) REVERT: C 158 ASP cc_start: 0.8496 (p0) cc_final: 0.8128 (t0) outliers start: 12 outliers final: 9 residues processed: 55 average time/residue: 0.2614 time to fit residues: 19.8429 Evaluate side-chains 50 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 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 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: 1.9990 chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.0870 overall best weight: 0.5760 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.088189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.070498 restraints weight = 40378.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.072472 restraints weight = 22213.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.073757 restraints weight = 14978.239| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8242 Z= 0.176 Angle : 0.613 9.591 11198 Z= 0.306 Chirality : 0.045 0.295 1274 Planarity : 0.004 0.047 1432 Dihedral : 8.091 58.840 1458 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.48 % Allowed : 14.71 % 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: 0.37 (0.28), residues: 955 helix: 0.69 (2.03), residues: 7 sheet: 1.04 (0.25), residues: 453 loop : -0.52 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 487 HIS 0.003 0.001 HIS C 287 PHE 0.017 0.001 PHE C 101 TYR 0.018 0.001 TYR B 548 ARG 0.004 0.000 ARG C 284 *********************** 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 54 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 509 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8212 (mmm-85) REVERT: C 128 PHE cc_start: 0.7066 (OUTLIER) cc_final: 0.6303 (t80) REVERT: C 158 ASP cc_start: 0.8593 (p0) cc_final: 0.8174 (t0) REVERT: C 320 ARG cc_start: 0.7628 (ttp-110) cc_final: 0.7415 (ttm170) outliers start: 13 outliers final: 10 residues processed: 54 average time/residue: 0.2520 time to fit residues: 18.5031 Evaluate side-chains 48 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 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 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: 6.9990 chunk 33 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.086962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.069956 restraints weight = 40521.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.071804 restraints weight = 22186.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.073019 restraints weight = 14899.722| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8242 Z= 0.282 Angle : 0.666 9.550 11198 Z= 0.336 Chirality : 0.046 0.288 1274 Planarity : 0.004 0.056 1432 Dihedral : 8.292 58.979 1458 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.37 % Allowed : 15.28 % 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: 0.14 (0.28), residues: 955 helix: -0.61 (1.90), residues: 6 sheet: 0.78 (0.25), residues: 447 loop : -0.51 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 487 HIS 0.004 0.001 HIS A 568 PHE 0.013 0.002 PHE B 304 TYR 0.013 0.001 TYR C 103 ARG 0.018 0.001 ARG A 399 ********************** 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 51 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 128 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6551 (t80) REVERT: C 158 ASP cc_start: 0.8549 (p0) cc_final: 0.8143 (t0) outliers start: 12 outliers final: 10 residues processed: 51 average time/residue: 0.2329 time to fit residues: 16.4665 Evaluate side-chains 48 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 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 38 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 70 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.088631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.071570 restraints weight = 40690.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.073519 restraints weight = 22098.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.074786 restraints weight = 14734.886| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8242 Z= 0.175 Angle : 0.626 9.423 11198 Z= 0.314 Chirality : 0.045 0.279 1274 Planarity : 0.004 0.047 1432 Dihedral : 8.192 59.099 1458 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.14 % Allowed : 15.39 % Favored : 83.47 % 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: 0.69 (2.01), residues: 7 sheet: 0.76 (0.25), residues: 475 loop : -0.45 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 487 HIS 0.003 0.001 HIS C 287 PHE 0.010 0.001 PHE B 340 TYR 0.013 0.001 TYR C 174 ARG 0.011 0.001 ARG A 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2917.67 seconds wall clock time: 53 minutes 13.86 seconds (3193.86 seconds total)