Starting phenix.real_space_refine on Wed Mar 12 16:54:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vse_43497/03_2025/8vse_43497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vse_43497/03_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_43497/03_2025/8vse_43497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vse_43497/03_2025/8vse_43497.map" model { file = "/net/cci-nas-00/data/ceres_data/8vse_43497/03_2025/8vse_43497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vse_43497/03_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-5624/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: 5.43, per 1000 atoms: 0.68 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: 2.06 Conformation dependent library (CDL) restraints added in 921.2 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: 1.00 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: 2.54 Time building geometry restraints manager: 2.46 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: 1.520 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.160 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.400 ------------------------------------------------------------------------------- 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 : 0.929 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: 0.3010 time to fit residues: 58.9474 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 : 0.944 ------------------------------------------------------------------------------- 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: 0.8980 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.098685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.080350 restraints weight = 46473.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.082191 restraints weight = 27029.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.083208 restraints weight = 18967.038| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8242 Z= 0.315 Angle : 0.728 11.609 11198 Z= 0.365 Chirality : 0.046 0.315 1274 Planarity : 0.005 0.046 1432 Dihedral : 8.162 58.536 1463 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.39 % Allowed : 10.83 % Favored : 86.77 % 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: 0.97 (0.28), residues: 955 helix: -0.49 (2.11), residues: 6 sheet: 1.56 (0.25), residues: 455 loop : -0.23 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 120 HIS 0.015 0.001 HIS B 532 PHE 0.017 0.002 PHE B 420 TYR 0.017 0.002 TYR C 174 ARG 0.007 0.001 ARG C 318 *********************** 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 84 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.4615 (OUTLIER) cc_final: 0.4310 (tp) REVERT: A 389 SER cc_start: 0.8135 (m) cc_final: 0.7724 (p) REVERT: A 409 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8496 (p) REVERT: B 299 PRO cc_start: 0.8274 (Cg_endo) cc_final: 0.7950 (Cg_exo) REVERT: B 509 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7839 (mmm160) REVERT: B 559 TYR cc_start: 0.7736 (m-80) cc_final: 0.7470 (m-10) REVERT: C 260 VAL cc_start: 0.9042 (t) cc_final: 0.8789 (p) REVERT: C 284 ARG cc_start: 0.8200 (mpp-170) cc_final: 0.7547 (ptt90) REVERT: C 320 ARG cc_start: 0.7243 (ttp80) cc_final: 0.7016 (ttp80) outliers start: 21 outliers final: 11 residues processed: 84 average time/residue: 0.2514 time to fit residues: 27.6529 Evaluate side-chains 62 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 48 CYS 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: 2.9990 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 261 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 = 0.4010 r_free = 0.4010 target = 0.088215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.070787 restraints weight = 41362.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.072665 restraints weight = 22738.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.073843 restraints weight = 15417.652| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8242 Z= 0.373 Angle : 0.746 9.734 11198 Z= 0.379 Chirality : 0.047 0.312 1274 Planarity : 0.005 0.050 1432 Dihedral : 8.481 59.895 1459 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.51 % Allowed : 12.20 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.28), residues: 955 helix: -0.71 (1.93), residues: 6 sheet: 0.98 (0.24), residues: 469 loop : -0.55 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 487 HIS 0.007 0.002 HIS B 532 PHE 0.026 0.003 PHE B 420 TYR 0.022 0.002 TYR C 319 ARG 0.007 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 74 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8742 (t) REVERT: B 349 ASN cc_start: 0.7858 (t0) cc_final: 0.7591 (t0) REVERT: B 509 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8124 (mmm160) REVERT: C 128 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6888 (t80) REVERT: C 170 GLN cc_start: 0.8334 (mp10) cc_final: 0.8115 (mp10) REVERT: C 284 ARG cc_start: 0.8322 (mpp-170) cc_final: 0.8068 (mpp-170) REVERT: C 320 ARG cc_start: 0.7302 (ttp80) cc_final: 0.6980 (mtm-85) outliers start: 22 outliers final: 14 residues processed: 71 average time/residue: 0.2375 time to fit residues: 22.9099 Evaluate side-chains 62 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 81 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 0.4980 chunk 3 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 HIS B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.088358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.071269 restraints weight = 39924.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.073179 restraints weight = 21930.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.074414 restraints weight = 14769.723| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8242 Z= 0.278 Angle : 0.665 9.779 11198 Z= 0.337 Chirality : 0.046 0.307 1274 Planarity : 0.004 0.049 1432 Dihedral : 8.387 59.379 1459 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.28 % Allowed : 12.88 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.28), residues: 955 helix: -0.53 (2.00), residues: 6 sheet: 0.81 (0.24), residues: 475 loop : -0.47 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 487 HIS 0.006 0.001 HIS A 361 PHE 0.013 0.002 PHE B 376 TYR 0.011 0.001 TYR A 548 ARG 0.005 0.001 ARG C 38 *********************** 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 66 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.4799 (mpp) cc_final: 0.4543 (mpp) REVERT: A 409 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8728 (t) REVERT: B 509 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8130 (mmm160) REVERT: C 104 MET cc_start: 0.7606 (pmm) cc_final: 0.7089 (tpt) REVERT: C 124 ASP cc_start: 0.8396 (t70) cc_final: 0.8128 (t0) REVERT: C 128 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6647 (t80) REVERT: C 170 GLN cc_start: 0.8340 (mp10) cc_final: 0.8056 (mp10) REVERT: C 177 THR cc_start: 0.8796 (m) cc_final: 0.8462 (p) REVERT: C 284 ARG cc_start: 0.8253 (mpp-170) cc_final: 0.7997 (mpp-170) REVERT: C 320 ARG cc_start: 0.7279 (ttp80) cc_final: 0.6921 (mtm-85) outliers start: 20 outliers final: 13 residues processed: 64 average time/residue: 0.2091 time to fit residues: 18.7912 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 : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 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 240 ASN Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 321 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 67 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 35 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.095302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.077275 restraints weight = 46340.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.079074 restraints weight = 26294.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.080203 restraints weight = 18303.775| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8242 Z= 0.213 Angle : 0.630 9.776 11198 Z= 0.316 Chirality : 0.045 0.305 1274 Planarity : 0.004 0.048 1432 Dihedral : 8.307 59.605 1458 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % 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: 0.26 (0.28), residues: 955 helix: -2.75 (1.23), residues: 12 sheet: 0.92 (0.24), residues: 466 loop : -0.49 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 487 HIS 0.003 0.001 HIS B 500 PHE 0.010 0.001 PHE A 376 TYR 0.022 0.001 TYR C 174 ARG 0.003 0.001 ARG C 38 *********************** 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 : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8697 (t) REVERT: B 448 LYS cc_start: 0.9114 (tppt) cc_final: 0.8808 (tppt) REVERT: B 509 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8120 (mmm160) REVERT: C 104 MET cc_start: 0.7737 (pmm) cc_final: 0.7083 (tpt) REVERT: C 128 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6467 (t80) REVERT: C 158 ASP cc_start: 0.8358 (p0) cc_final: 0.8083 (t0) REVERT: C 170 GLN cc_start: 0.8318 (mp10) cc_final: 0.8075 (mp10) REVERT: C 284 ARG cc_start: 0.8336 (mpp-170) cc_final: 0.8051 (mpp-170) REVERT: C 320 ARG cc_start: 0.7349 (ttp80) cc_final: 0.6965 (mtm-85) outliers start: 20 outliers final: 11 residues processed: 68 average time/residue: 0.2168 time to fit residues: 20.4774 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 : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** 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 = 0.3982 r_free = 0.3982 target = 0.086564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.069308 restraints weight = 39717.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.071226 restraints weight = 21938.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.072438 restraints weight = 14801.121| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4596 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= 0.340 Angle : 0.717 11.621 11198 Z= 0.363 Chirality : 0.046 0.286 1274 Planarity : 0.005 0.049 1432 Dihedral : 8.549 59.261 1458 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % 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: -0.14 (0.27), residues: 955 helix: -2.72 (1.18), residues: 12 sheet: 0.65 (0.24), residues: 446 loop : -0.70 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 487 HIS 0.007 0.001 HIS A 568 PHE 0.015 0.002 PHE C 101 TYR 0.016 0.002 TYR C 174 ARG 0.005 0.001 ARG B 504 *********************** 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 62 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8573 (tm-30) REVERT: B 445 GLN cc_start: 0.8910 (pm20) cc_final: 0.8616 (pm20) REVERT: B 448 LYS cc_start: 0.9190 (tppt) cc_final: 0.8839 (tppt) REVERT: B 509 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8141 (mmm160) REVERT: C 128 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6633 (t80) REVERT: C 158 ASP cc_start: 0.8430 (p0) cc_final: 0.8035 (t0) REVERT: C 170 GLN cc_start: 0.8419 (mp10) cc_final: 0.8176 (mp10) REVERT: C 284 ARG cc_start: 0.8538 (mpp-170) cc_final: 0.8170 (mpp-170) REVERT: C 320 ARG cc_start: 0.7320 (ttp80) cc_final: 0.6971 (mtm-85) outliers start: 18 outliers final: 11 residues processed: 62 average time/residue: 0.2218 time to fit residues: 19.1912 Evaluate side-chains 56 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 47 optimal weight: 0.0040 chunk 49 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 chunk 80 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.086875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.069777 restraints weight = 39619.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.071618 restraints weight = 21985.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.072813 restraints weight = 14845.880| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8242 Z= 0.263 Angle : 0.656 9.574 11198 Z= 0.332 Chirality : 0.046 0.282 1274 Planarity : 0.004 0.050 1432 Dihedral : 8.519 59.429 1458 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % 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: -0.16 (0.27), residues: 955 helix: -2.67 (1.19), residues: 12 sheet: 0.61 (0.24), residues: 448 loop : -0.70 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 487 HIS 0.003 0.001 HIS C 287 PHE 0.013 0.002 PHE A 420 TYR 0.019 0.002 TYR B 548 ARG 0.002 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8553 (tm-30) REVERT: B 509 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8179 (mmm-85) REVERT: C 104 MET cc_start: 0.7828 (pmm) cc_final: 0.6922 (tpt) REVERT: C 128 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6433 (t80) REVERT: C 158 ASP cc_start: 0.8467 (p0) cc_final: 0.8036 (t0) REVERT: C 170 GLN cc_start: 0.8420 (mp10) cc_final: 0.8170 (mp10) REVERT: C 284 ARG cc_start: 0.8583 (mpp-170) cc_final: 0.8214 (mpp-170) REVERT: C 320 ARG cc_start: 0.7314 (ttp80) cc_final: 0.6966 (mtm-85) outliers start: 16 outliers final: 13 residues processed: 57 average time/residue: 0.2252 time to fit residues: 17.8848 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 : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL 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 498 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 473 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 35 optimal weight: 30.0000 chunk 32 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.087084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.069708 restraints weight = 39297.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.071673 restraints weight = 21717.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.072918 restraints weight = 14634.385| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4712 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= 0.201 Angle : 0.630 9.571 11198 Z= 0.318 Chirality : 0.045 0.288 1274 Planarity : 0.004 0.048 1432 Dihedral : 8.423 58.409 1458 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.94 % Allowed : 15.17 % Favored : 82.90 % 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 (0.27), residues: 955 helix: -2.54 (1.23), residues: 12 sheet: 0.65 (0.24), residues: 454 loop : -0.63 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 487 HIS 0.003 0.001 HIS C 287 PHE 0.016 0.002 PHE C 155 TYR 0.013 0.001 TYR C 174 ARG 0.003 0.001 ARG C 38 *********************** 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 61 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 509 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8174 (mmm-85) REVERT: C 104 MET cc_start: 0.7941 (pmm) cc_final: 0.6936 (tpt) REVERT: C 128 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6388 (t80) REVERT: C 158 ASP cc_start: 0.8513 (p0) cc_final: 0.8036 (t0) REVERT: C 170 GLN cc_start: 0.8368 (mp10) cc_final: 0.8138 (mp10) REVERT: C 176 VAL cc_start: 0.8704 (t) cc_final: 0.8295 (m) REVERT: C 284 ARG cc_start: 0.8565 (mpp-170) cc_final: 0.8213 (mpp-170) REVERT: C 320 ARG cc_start: 0.7105 (ttp80) cc_final: 0.6786 (mtm-85) outliers start: 17 outliers final: 12 residues processed: 59 average time/residue: 0.2115 time to fit residues: 17.4204 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 : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.084556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.067316 restraints weight = 39628.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.069233 restraints weight = 21565.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.070476 restraints weight = 14492.275| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 8242 Z= 0.384 Angle : 0.740 9.643 11198 Z= 0.375 Chirality : 0.047 0.275 1274 Planarity : 0.005 0.052 1432 Dihedral : 8.915 59.714 1458 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.51 % Allowed : 14.48 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.49 (0.27), residues: 955 helix: -2.37 (1.25), residues: 12 sheet: 0.30 (0.24), residues: 448 loop : -0.83 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 487 HIS 0.005 0.001 HIS A 568 PHE 0.022 0.002 PHE B 376 TYR 0.014 0.002 TYR A 548 ARG 0.005 0.001 ARG B 504 *********************** 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 62 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 40 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8605 (tm-30) REVERT: B 509 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8257 (mmm-85) REVERT: C 100 VAL cc_start: 0.9194 (t) cc_final: 0.8961 (m) REVERT: C 104 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7590 (pmm) REVERT: C 128 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.6715 (t80) REVERT: C 158 ASP cc_start: 0.8633 (p0) cc_final: 0.8044 (t70) REVERT: C 170 GLN cc_start: 0.8458 (mp10) cc_final: 0.8180 (mp10) REVERT: C 176 VAL cc_start: 0.8805 (t) cc_final: 0.8351 (m) REVERT: C 284 ARG cc_start: 0.8905 (mpp-170) cc_final: 0.8405 (mpp-170) outliers start: 22 outliers final: 15 residues processed: 60 average time/residue: 0.2162 time to fit residues: 18.4281 Evaluate side-chains 57 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 307 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 94 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.086150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.068913 restraints weight = 39532.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.070809 restraints weight = 21621.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.072075 restraints weight = 14546.808| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5075 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= 0.206 Angle : 0.659 9.372 11198 Z= 0.331 Chirality : 0.046 0.270 1274 Planarity : 0.004 0.049 1432 Dihedral : 8.705 58.922 1458 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.17 % Allowed : 15.39 % Favored : 82.44 % 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: -0.34 (0.28), residues: 955 helix: -1.47 (1.42), residues: 13 sheet: 0.34 (0.24), residues: 464 loop : -0.72 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 120 HIS 0.004 0.001 HIS C 287 PHE 0.018 0.002 PHE C 155 TYR 0.017 0.001 TYR C 174 ARG 0.004 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 59 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8489 (tm-30) REVERT: A 427 GLU cc_start: 0.7580 (pm20) cc_final: 0.7343 (pm20) REVERT: A 493 MET cc_start: 0.3502 (ttt) cc_final: 0.3024 (ttt) REVERT: A 499 MET cc_start: 0.7320 (tpp) cc_final: 0.6906 (tpp) REVERT: B 509 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8185 (mmm-85) REVERT: C 100 VAL cc_start: 0.9129 (t) cc_final: 0.8889 (m) REVERT: C 128 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6487 (t80) REVERT: C 158 ASP cc_start: 0.8606 (p0) cc_final: 0.7997 (t70) REVERT: C 170 GLN cc_start: 0.8389 (mp10) cc_final: 0.8156 (mp10) REVERT: C 176 VAL cc_start: 0.8812 (t) cc_final: 0.8434 (m) REVERT: C 284 ARG cc_start: 0.8741 (mpp-170) cc_final: 0.8255 (mpp-170) outliers start: 19 outliers final: 11 residues processed: 58 average time/residue: 0.2442 time to fit residues: 19.6017 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 : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 307 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 35 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.094013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.076033 restraints weight = 46539.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.077742 restraints weight = 26518.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.078962 restraints weight = 18478.208| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5048 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= 0.191 Angle : 0.651 11.900 11198 Z= 0.323 Chirality : 0.046 0.283 1274 Planarity : 0.004 0.048 1432 Dihedral : 8.610 59.019 1458 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.48 % Allowed : 15.74 % 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: -0.24 (0.28), residues: 955 helix: -1.45 (1.43), residues: 13 sheet: 0.42 (0.24), residues: 466 loop : -0.67 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 120 HIS 0.003 0.001 HIS A 568 PHE 0.017 0.001 PHE C 155 TYR 0.018 0.001 TYR C 174 ARG 0.003 0.000 ARG A 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2981.65 seconds wall clock time: 52 minutes 34.71 seconds (3154.71 seconds total)