Starting phenix.real_space_refine on Sun Aug 24 06:30:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vsc_43493/08_2025/8vsc_43493.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vsc_43493/08_2025/8vsc_43493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vsc_43493/08_2025/8vsc_43493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vsc_43493/08_2025/8vsc_43493.map" model { file = "/net/cci-nas-00/data/ceres_data/8vsc_43493/08_2025/8vsc_43493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vsc_43493/08_2025/8vsc_43493.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.055 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: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 5625 2.51 5 N 1550 2.21 5 O 1617 1.98 5 H 8786 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17630 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 4792 Classifications: {'peptide': 297} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 275} Chain breaks: 6 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 4980 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 288} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 7858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 7858 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 29, 'TRANS': 502} Chain breaks: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 8, 'GLN:plan1': 3, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 3.20, per 1000 atoms: 0.18 Number of scatterers: 17630 At special positions: 0 Unit cell: (97.578, 105.918, 128.436, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1617 8.00 N 1550 7.00 C 5625 6.00 H 8786 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS I 350 " distance=2.03 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS I 211 " distance=2.05 Simple disulfide: pdb=" SG CYS B 264 " - pdb=" SG CYS B 327 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 297 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS I 26 " - pdb=" SG CYS I 35 " distance=2.03 Simple disulfide: pdb=" SG CYS I 425 " - pdb=" SG CYS I 436 " 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 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 648.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 17.5% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 8 through 28 Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 108 through 115 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 171 through 182 Processing helix chain 'A' and resid 235 through 240 removed outlier: 4.692A pdb=" N GLN A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.878A pdb=" N VAL B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 28 " --> pdb=" O ILE B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 171 through 182 Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 313 through 318 Processing helix chain 'I' and resid 65 through 70 removed outlier: 3.923A pdb=" N LEU I 69 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 3.572A pdb=" N ALA I 95 " --> pdb=" O GLY I 91 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU I 96 " --> pdb=" O ALA I 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 91 through 96' Processing helix chain 'I' and resid 108 through 112 Processing helix chain 'I' and resid 140 through 145 removed outlier: 3.700A pdb=" N LEU I 145 " --> pdb=" O LEU I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 338 removed outlier: 3.930A pdb=" N LEU I 335 " --> pdb=" O PRO I 331 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU I 336 " --> pdb=" O ASP I 332 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS I 337 " --> pdb=" O SER I 333 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU I 338 " --> pdb=" O PHE I 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 331 through 338' Processing helix chain 'I' and resid 486 through 490 removed outlier: 3.586A pdb=" N GLU I 490 " --> pdb=" O GLY I 487 " (cutoff:3.500A) Processing helix chain 'I' and resid 509 through 513 Processing helix chain 'I' and resid 552 through 557 Processing helix chain 'I' and resid 558 through 562 removed outlier: 3.599A pdb=" N THR I 561 " --> pdb=" O GLY I 558 " (cutoff:3.500A) Processing helix chain 'I' and resid 579 through 585 removed outlier: 4.288A pdb=" N ALA I 583 " --> pdb=" O GLY I 579 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 170 removed outlier: 3.774A pdb=" N GLU A 125 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE A 228 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL B 347 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 10.430A pdb=" N ARG A 81 " --> pdb=" O PRO B 345 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS B 344 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL B 341 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN B 352 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLU B 333 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 354 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA B 331 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ARG B 356 " --> pdb=" O PRO B 329 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N CYS B 358 " --> pdb=" O CYS B 327 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N CYS B 327 " --> pdb=" O CYS B 358 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N TYR B 340 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE B 282 " --> pdb=" O TYR B 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 107 removed outlier: 3.851A pdb=" N GLY A 187 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 154 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLN A 143 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR A 152 " --> pdb=" O GLN A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 268 Processing sheet with id=AA4, first strand: chain 'A' and resid 282 through 284 removed outlier: 7.381A pdb=" N ILE A 282 " --> pdb=" O TYR A 340 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR A 340 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 284 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER A 357 " --> pdb=" O GLN A 330 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A 332 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 355 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N MET A 353 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N SER A 351 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 9.670A pdb=" N VAL A 338 " --> pdb=" O GLN A 349 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N GLN A 349 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 9.685A pdb=" N TYR A 340 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N VAL A 347 " --> pdb=" O TYR A 340 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N ARG B 81 " --> pdb=" O PRO A 345 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL A 347 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE B 228 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU B 126 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 230 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA B 124 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N MET B 232 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 165 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 107 removed outlier: 5.550A pdb=" N GLY B 187 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLN B 137 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU B 157 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL B 139 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASN B 155 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU B 141 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 265 through 267 Processing sheet with id=AA7, first strand: chain 'B' and resid 271 through 272 Processing sheet with id=AA8, first strand: chain 'I' and resid 27 through 29 removed outlier: 7.279A pdb=" N LEU I 54 " --> pdb=" O ASP I 79 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU I 129 " --> pdb=" O SER I 155 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN I 271 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU I 344 " --> pdb=" O ASP I 369 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU I 368 " --> pdb=" O LEU I 392 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU I 391 " --> pdb=" O ASN I 416 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU I 496 " --> pdb=" O ASN I 520 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 63 through 64 Processing sheet with id=AB1, first strand: chain 'I' and resid 163 through 164 Processing sheet with id=AB2, first strand: chain 'I' and resid 211 through 212 Processing sheet with id=AB3, first strand: chain 'I' and resid 353 through 354 removed outlier: 3.581A pdb=" N PHE I 354 " --> pdb=" O THR I 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'I' and resid 457 through 458 218 hydrogen bonds defined for protein. 597 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: 3.68 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 8778 1.04 - 1.25: 1451 1.25 - 1.46: 2593 1.46 - 1.66: 4920 1.66 - 1.87: 70 Bond restraints: 17812 Sorted by residual: bond pdb=" CB CYS B 4 " pdb=" SG CYS B 4 " ideal model delta sigma weight residual 1.808 1.730 0.078 3.30e-02 9.18e+02 5.61e+00 bond pdb=" CG PRO I 511 " pdb=" CD PRO I 511 " ideal model delta sigma weight residual 1.503 1.429 0.074 3.40e-02 8.65e+02 4.76e+00 bond pdb=" C LEU I 362 " pdb=" O LEU I 362 " ideal model delta sigma weight residual 1.235 1.243 -0.009 4.70e-03 4.53e+04 3.30e+00 bond pdb=" CB CYS I 211 " pdb=" SG CYS I 211 " ideal model delta sigma weight residual 1.808 1.868 -0.060 3.30e-02 9.18e+02 3.30e+00 bond pdb=" N THR A 3 " pdb=" CA THR A 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 ... (remaining 17807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 32000 2.49 - 4.99: 239 4.99 - 7.48: 13 7.48 - 9.98: 1 9.98 - 12.47: 2 Bond angle restraints: 32255 Sorted by residual: angle pdb=" CA PRO I 511 " pdb=" N PRO I 511 " pdb=" CD PRO I 511 " ideal model delta sigma weight residual 112.00 102.36 9.64 1.40e+00 5.10e-01 4.74e+01 angle pdb=" CA CYS B 4 " pdb=" CB CYS B 4 " pdb=" SG CYS B 4 " ideal model delta sigma weight residual 114.40 126.87 -12.47 2.30e+00 1.89e-01 2.94e+01 angle pdb=" N PRO I 511 " pdb=" CD PRO I 511 " pdb=" CG PRO I 511 " ideal model delta sigma weight residual 103.20 96.69 6.51 1.50e+00 4.44e-01 1.88e+01 angle pdb=" CB MET I 556 " pdb=" CG MET I 556 " pdb=" SD MET I 556 " ideal model delta sigma weight residual 112.70 124.25 -11.55 3.00e+00 1.11e-01 1.48e+01 angle pdb=" N CYS B 4 " pdb=" CA CYS B 4 " pdb=" CB CYS B 4 " ideal model delta sigma weight residual 109.69 104.79 4.90 1.53e+00 4.27e-01 1.03e+01 ... (remaining 32250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 7513 17.69 - 35.38: 636 35.38 - 53.06: 200 53.06 - 70.75: 57 70.75 - 88.44: 31 Dihedral angle restraints: 8437 sinusoidal: 4643 harmonic: 3794 Sorted by residual: dihedral pdb=" CB CYS A 326 " pdb=" SG CYS A 326 " pdb=" SG CYS B 326 " pdb=" CB CYS B 326 " ideal model delta sinusoidal sigma weight residual -86.00 -156.40 70.40 1 1.00e+01 1.00e-02 6.38e+01 dihedral pdb=" CB CYS B 4 " pdb=" SG CYS B 4 " pdb=" SG CYS I 211 " pdb=" CB CYS I 211 " ideal model delta sinusoidal sigma weight residual 93.00 53.03 39.97 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CA LEU B 133 " pdb=" C LEU B 133 " pdb=" N LYS B 134 " pdb=" CA LYS B 134 " ideal model delta harmonic sigma weight residual 180.00 -156.89 -23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 8434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 853 0.031 - 0.062: 410 0.062 - 0.092: 66 0.092 - 0.123: 62 0.123 - 0.154: 14 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA ILE I 188 " pdb=" N ILE I 188 " pdb=" C ILE I 188 " pdb=" CB ILE I 188 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CG LEU I 506 " pdb=" CB LEU I 506 " pdb=" CD1 LEU I 506 " pdb=" CD2 LEU I 506 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA ILE I 330 " pdb=" N ILE I 330 " pdb=" C ILE I 330 " pdb=" CB ILE I 330 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 1402 not shown) Planarity restraints: 2635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU I 510 " 0.077 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO I 511 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO I 511 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO I 511 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 343 " -0.266 9.50e-02 1.11e+02 8.92e-02 9.72e+00 pdb=" NE ARG A 343 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 343 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 343 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 343 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 343 " 0.007 2.00e-02 2.50e+03 pdb="HH12 ARG A 343 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 343 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 343 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 318 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO A 319 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 319 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 319 " 0.025 5.00e-02 4.00e+02 ... (remaining 2632 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 2417 2.26 - 2.84: 39990 2.84 - 3.43: 45754 3.43 - 4.01: 65134 4.01 - 4.60: 98569 Nonbonded interactions: 251864 Sorted by model distance: nonbonded pdb=" OE2 GLU B 333 " pdb=" HE ARG B 356 " model vdw 1.672 2.450 nonbonded pdb=" OE1 GLU A 10 " pdb="HH21 ARG A 14 " model vdw 1.690 2.450 nonbonded pdb=" O MET A 84 " pdb="HH12 ARG A 226 " model vdw 1.692 2.450 nonbonded pdb=" O PRO A 298 " pdb=" HH TYR A 314 " model vdw 1.693 2.450 nonbonded pdb=" O HIS A 283 " pdb=" HZ1 LYS A 286 " model vdw 1.701 2.450 ... (remaining 251859 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 3 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name H or name HA or name HB2 or na \ me HB3 or name HG2 or name HG3)) or resid 6 or (resid 7 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 8 through 197 or \ resid 206 through 210 or resid 224 through 361)) selection = (chain 'B' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 4 through 59 or resid 73 through 132 or resid 13 \ 4 through 197 or resid 206 through 240 or resid 262 through 299 or resid 314 thr \ ough 361)) } 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 individual isotropic 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: 3.140 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: 0.080 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.120 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 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 : 0.004 0.078 9039 Z= 0.161 Angle : 0.740 12.470 12284 Z= 0.395 Chirality : 0.041 0.154 1405 Planarity : 0.006 0.117 1582 Dihedral : 14.825 88.438 3343 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.42 % Allowed : 15.07 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.25), residues: 1109 helix: -0.45 (0.42), residues: 137 sheet: -1.53 (0.29), residues: 302 loop : -0.24 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 343 TYR 0.015 0.001 TYR A 142 PHE 0.014 0.001 PHE B 95 TRP 0.009 0.001 TRP I 247 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9026) covalent geometry : angle 0.73398 (12258) SS BOND : bond 0.00448 ( 13) SS BOND : angle 2.20352 ( 26) hydrogen bonds : bond 0.21913 ( 218) hydrogen bonds : angle 8.61540 ( 597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 3 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 366 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue THR 466 is missing expected H atoms. Skipping. Residue SER 527 is missing expected H atoms. Skipping. Residue THR 533 is missing expected H atoms. Skipping. Residue VAL 536 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 590 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 556 MET cc_start: 0.7116 (ppp) cc_final: 0.6513 (ppp) outliers start: 4 outliers final: 4 residues processed: 86 average time/residue: 0.7552 time to fit residues: 71.1608 Evaluate side-chains 79 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 353 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.0670 chunk 106 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN I 584 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.209264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.167640 restraints weight = 27683.149| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.19 r_work: 0.3897 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9039 Z= 0.131 Angle : 0.584 5.795 12284 Z= 0.301 Chirality : 0.040 0.167 1405 Planarity : 0.005 0.056 1582 Dihedral : 5.915 71.262 1236 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.98 % Allowed : 12.89 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.25), residues: 1109 helix: -0.01 (0.43), residues: 135 sheet: -1.59 (0.28), residues: 314 loop : -0.34 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 343 TYR 0.016 0.001 TYR A 142 PHE 0.013 0.001 PHE B 188 TRP 0.005 0.001 TRP A 150 HIS 0.003 0.001 HIS I 106 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9026) covalent geometry : angle 0.58152 (12258) SS BOND : bond 0.00403 ( 13) SS BOND : angle 1.26906 ( 26) hydrogen bonds : bond 0.05840 ( 218) hydrogen bonds : angle 7.05798 ( 597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 3 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 366 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue THR 466 is missing expected H atoms. Skipping. Residue SER 527 is missing expected H atoms. Skipping. Residue THR 533 is missing expected H atoms. Skipping. Residue VAL 536 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 590 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8401 (ttt-90) REVERT: A 97 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7056 (pt0) REVERT: B 263 ASN cc_start: 0.7104 (p0) cc_final: 0.6760 (p0) REVERT: I 231 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7271 (mt-10) outliers start: 19 outliers final: 4 residues processed: 93 average time/residue: 0.9427 time to fit residues: 94.8995 Evaluate side-chains 85 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 231 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4459 r_free = 0.4459 target = 0.204476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.162976 restraints weight = 27891.235| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.12 r_work: 0.3842 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9039 Z= 0.225 Angle : 0.628 6.327 12284 Z= 0.322 Chirality : 0.042 0.159 1405 Planarity : 0.005 0.043 1582 Dihedral : 5.973 71.791 1231 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.91 % Allowed : 12.99 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.25), residues: 1109 helix: 0.10 (0.44), residues: 135 sheet: -1.84 (0.27), residues: 316 loop : -0.62 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 343 TYR 0.019 0.002 TYR A 142 PHE 0.017 0.002 PHE B 188 TRP 0.008 0.001 TRP A 281 HIS 0.004 0.001 HIS I 106 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 9026) covalent geometry : angle 0.62347 (12258) SS BOND : bond 0.00487 ( 13) SS BOND : angle 1.79018 ( 26) hydrogen bonds : bond 0.05610 ( 218) hydrogen bonds : angle 6.73963 ( 597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 3 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 366 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue THR 466 is missing expected H atoms. Skipping. Residue SER 527 is missing expected H atoms. Skipping. Residue THR 533 is missing expected H atoms. Skipping. Residue VAL 536 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 590 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8447 (ttt-90) REVERT: A 97 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7159 (tm130) REVERT: A 338 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8131 (p) REVERT: B 263 ASN cc_start: 0.7164 (p0) cc_final: 0.6930 (p0) REVERT: I 231 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: I 475 SER cc_start: 0.7842 (OUTLIER) cc_final: 0.7574 (m) REVERT: I 510 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8148 (tt) outliers start: 28 outliers final: 10 residues processed: 100 average time/residue: 1.0169 time to fit residues: 110.7064 Evaluate side-chains 93 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 376 GLU Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 475 SER Chi-restraints excluded: chain I residue 510 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 chunk 76 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.206698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.165460 restraints weight = 27791.467| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.13 r_work: 0.3877 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9039 Z= 0.118 Angle : 0.562 6.392 12284 Z= 0.286 Chirality : 0.040 0.159 1405 Planarity : 0.004 0.041 1582 Dihedral : 5.633 70.071 1231 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.29 % Allowed : 14.14 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.25), residues: 1109 helix: 0.35 (0.45), residues: 135 sheet: -1.83 (0.27), residues: 316 loop : -0.46 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 16 TYR 0.014 0.001 TYR A 142 PHE 0.013 0.001 PHE B 188 TRP 0.005 0.001 TRP A 281 HIS 0.003 0.001 HIS I 372 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9026) covalent geometry : angle 0.55594 (12258) SS BOND : bond 0.00310 ( 13) SS BOND : angle 1.87465 ( 26) hydrogen bonds : bond 0.04607 ( 218) hydrogen bonds : angle 6.54715 ( 597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 3 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 366 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue THR 466 is missing expected H atoms. Skipping. Residue SER 527 is missing expected H atoms. Skipping. Residue THR 533 is missing expected H atoms. Skipping. Residue VAL 536 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 590 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8393 (ttt-90) REVERT: A 97 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.7141 (tm130) REVERT: A 130 ARG cc_start: 0.7700 (ttp-110) cc_final: 0.7238 (ttm170) REVERT: A 177 GLN cc_start: 0.6414 (pp30) cc_final: 0.6098 (pp30) REVERT: A 338 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.8080 (p) REVERT: B 263 ASN cc_start: 0.7150 (p0) cc_final: 0.6905 (p0) REVERT: I 231 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: I 510 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8115 (tt) outliers start: 22 outliers final: 13 residues processed: 98 average time/residue: 0.8848 time to fit residues: 94.4767 Evaluate side-chains 96 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 376 GLU Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 400 ASP Chi-restraints excluded: chain I residue 445 LEU Chi-restraints excluded: chain I residue 510 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.205116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.163869 restraints weight = 27773.913| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.11 r_work: 0.3860 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9039 Z= 0.164 Angle : 0.573 6.295 12284 Z= 0.293 Chirality : 0.040 0.158 1405 Planarity : 0.004 0.040 1582 Dihedral : 5.452 69.575 1229 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.12 % Allowed : 14.24 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.25), residues: 1109 helix: 0.32 (0.45), residues: 136 sheet: -1.83 (0.28), residues: 316 loop : -0.52 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 343 TYR 0.016 0.002 TYR A 142 PHE 0.014 0.001 PHE B 188 TRP 0.006 0.001 TRP B 178 HIS 0.003 0.001 HIS I 181 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9026) covalent geometry : angle 0.56974 (12258) SS BOND : bond 0.00320 ( 13) SS BOND : angle 1.48874 ( 26) hydrogen bonds : bond 0.04609 ( 218) hydrogen bonds : angle 6.40384 ( 597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 3 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 366 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue THR 466 is missing expected H atoms. Skipping. Residue SER 527 is missing expected H atoms. Skipping. Residue THR 533 is missing expected H atoms. Skipping. Residue VAL 536 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 590 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8435 (ttt-90) REVERT: A 97 GLN cc_start: 0.7413 (pp30) cc_final: 0.7180 (tm130) REVERT: A 177 GLN cc_start: 0.6411 (pp30) cc_final: 0.6084 (pp30) REVERT: A 338 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8118 (p) REVERT: I 231 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: I 475 SER cc_start: 0.7659 (OUTLIER) cc_final: 0.7416 (m) outliers start: 30 outliers final: 16 residues processed: 101 average time/residue: 0.7475 time to fit residues: 83.0063 Evaluate side-chains 98 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 376 GLU Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 400 ASP Chi-restraints excluded: chain I residue 445 LEU Chi-restraints excluded: chain I residue 475 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 80 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 100 HIS B 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.205654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.164373 restraints weight = 27611.513| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.14 r_work: 0.3869 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9039 Z= 0.132 Angle : 0.555 6.682 12284 Z= 0.282 Chirality : 0.040 0.155 1405 Planarity : 0.004 0.042 1582 Dihedral : 5.314 68.293 1229 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.70 % Allowed : 15.07 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.25), residues: 1109 helix: 0.44 (0.46), residues: 136 sheet: -1.87 (0.28), residues: 317 loop : -0.44 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 343 TYR 0.013 0.001 TYR A 142 PHE 0.013 0.001 PHE B 188 TRP 0.006 0.001 TRP B 178 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9026) covalent geometry : angle 0.55089 (12258) SS BOND : bond 0.00255 ( 13) SS BOND : angle 1.54030 ( 26) hydrogen bonds : bond 0.04344 ( 218) hydrogen bonds : angle 6.32394 ( 597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 3 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 366 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue THR 466 is missing expected H atoms. Skipping. Residue SER 527 is missing expected H atoms. Skipping. Residue THR 533 is missing expected H atoms. Skipping. Residue VAL 536 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 590 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8204 (ttt-90) REVERT: A 97 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7214 (tm130) REVERT: A 177 GLN cc_start: 0.6424 (pp30) cc_final: 0.6156 (pp30) REVERT: I 231 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7324 (mt-10) REVERT: I 566 LEU cc_start: 0.7569 (tp) cc_final: 0.7367 (mp) outliers start: 26 outliers final: 15 residues processed: 106 average time/residue: 0.8262 time to fit residues: 96.2946 Evaluate side-chains 101 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 376 GLU Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 400 ASP Chi-restraints excluded: chain I residue 445 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 100 HIS B 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.205690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.164578 restraints weight = 27775.372| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.12 r_work: 0.3869 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9039 Z= 0.134 Angle : 0.558 7.131 12284 Z= 0.282 Chirality : 0.040 0.145 1405 Planarity : 0.004 0.039 1582 Dihedral : 5.258 67.099 1229 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.70 % Allowed : 15.90 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.25), residues: 1109 helix: 0.48 (0.46), residues: 136 sheet: -1.86 (0.28), residues: 317 loop : -0.45 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 343 TYR 0.023 0.002 TYR B 103 PHE 0.015 0.001 PHE B 188 TRP 0.007 0.001 TRP B 178 HIS 0.003 0.001 HIS I 372 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9026) covalent geometry : angle 0.55242 (12258) SS BOND : bond 0.00344 ( 13) SS BOND : angle 1.76858 ( 26) hydrogen bonds : bond 0.04245 ( 218) hydrogen bonds : angle 6.29961 ( 597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 3 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 366 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue THR 466 is missing expected H atoms. Skipping. Residue SER 527 is missing expected H atoms. Skipping. Residue THR 533 is missing expected H atoms. Skipping. Residue VAL 536 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 590 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8437 (tpt170) REVERT: A 177 GLN cc_start: 0.6447 (pp30) cc_final: 0.6178 (pp30) REVERT: I 189 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: I 231 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7346 (mt-10) outliers start: 26 outliers final: 15 residues processed: 100 average time/residue: 0.8624 time to fit residues: 94.4713 Evaluate side-chains 99 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 376 GLU Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 400 ASP Chi-restraints excluded: chain I residue 445 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 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 137 GLN B 100 HIS B 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.205071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.163768 restraints weight = 27768.555| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.13 r_work: 0.3853 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9039 Z= 0.158 Angle : 0.575 8.388 12284 Z= 0.291 Chirality : 0.040 0.141 1405 Planarity : 0.004 0.048 1582 Dihedral : 5.294 66.142 1229 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.49 % Allowed : 15.80 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.25), residues: 1109 helix: 0.46 (0.46), residues: 136 sheet: -1.91 (0.28), residues: 315 loop : -0.48 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 343 TYR 0.014 0.002 TYR A 142 PHE 0.021 0.002 PHE I 87 TRP 0.009 0.001 TRP B 178 HIS 0.003 0.001 HIS I 181 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9026) covalent geometry : angle 0.56916 (12258) SS BOND : bond 0.00296 ( 13) SS BOND : angle 1.90243 ( 26) hydrogen bonds : bond 0.04395 ( 218) hydrogen bonds : angle 6.25099 ( 597) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 3 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 366 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue THR 466 is missing expected H atoms. Skipping. Residue SER 527 is missing expected H atoms. Skipping. Residue THR 533 is missing expected H atoms. Skipping. Residue VAL 536 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 590 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8184 (ttt90) REVERT: A 123 ARG cc_start: 0.6736 (ttt-90) cc_final: 0.6206 (tpt-90) REVERT: A 177 GLN cc_start: 0.6428 (pp30) cc_final: 0.6161 (pp30) REVERT: I 231 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7357 (mt-10) outliers start: 24 outliers final: 15 residues processed: 95 average time/residue: 0.9151 time to fit residues: 94.4254 Evaluate side-chains 98 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 376 GLU Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 400 ASP Chi-restraints excluded: chain I residue 445 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 0.0980 chunk 48 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 81 optimal weight: 0.0070 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.205975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.165171 restraints weight = 27727.737| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.10 r_work: 0.3880 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9039 Z= 0.107 Angle : 0.541 9.265 12284 Z= 0.273 Chirality : 0.039 0.142 1405 Planarity : 0.004 0.046 1582 Dihedral : 5.093 63.455 1229 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.18 % Allowed : 16.63 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.26), residues: 1109 helix: 0.54 (0.46), residues: 136 sheet: -1.91 (0.28), residues: 315 loop : -0.36 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 343 TYR 0.014 0.001 TYR A 288 PHE 0.014 0.001 PHE B 95 TRP 0.009 0.001 TRP B 178 HIS 0.004 0.001 HIS I 372 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9026) covalent geometry : angle 0.53782 (12258) SS BOND : bond 0.00198 ( 13) SS BOND : angle 1.40483 ( 26) hydrogen bonds : bond 0.03992 ( 218) hydrogen bonds : angle 6.17134 ( 597) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 3 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 366 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue THR 466 is missing expected H atoms. Skipping. Residue SER 527 is missing expected H atoms. Skipping. Residue THR 533 is missing expected H atoms. Skipping. Residue VAL 536 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 590 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8474 (tpt170) REVERT: A 177 GLN cc_start: 0.6383 (pp30) cc_final: 0.6121 (pp30) REVERT: A 359 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8121 (pttm) REVERT: I 231 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7336 (mt-10) outliers start: 21 outliers final: 14 residues processed: 99 average time/residue: 0.8206 time to fit residues: 88.8382 Evaluate side-chains 100 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 376 GLU Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 400 ASP Chi-restraints excluded: chain I residue 445 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.0470 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.206399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.165275 restraints weight = 27613.468| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.14 r_work: 0.3874 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9039 Z= 0.125 Angle : 0.551 11.230 12284 Z= 0.277 Chirality : 0.039 0.142 1405 Planarity : 0.004 0.044 1582 Dihedral : 5.062 61.820 1229 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.77 % Allowed : 17.36 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.26), residues: 1109 helix: 0.55 (0.46), residues: 135 sheet: -1.84 (0.28), residues: 319 loop : -0.36 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 343 TYR 0.012 0.001 TYR A 142 PHE 0.013 0.001 PHE B 188 TRP 0.009 0.001 TRP B 178 HIS 0.003 0.001 HIS I 372 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9026) covalent geometry : angle 0.54766 (12258) SS BOND : bond 0.00241 ( 13) SS BOND : angle 1.37774 ( 26) hydrogen bonds : bond 0.04061 ( 218) hydrogen bonds : angle 6.11182 ( 597) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 3 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue ILE 7 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 315 is missing expected H atoms. Skipping. Residue LEU 329 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue MET 366 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Residue SER 434 is missing expected H atoms. Skipping. Residue THR 466 is missing expected H atoms. Skipping. Residue SER 527 is missing expected H atoms. Skipping. Residue THR 533 is missing expected H atoms. Skipping. Residue VAL 536 is missing expected H atoms. Skipping. Residue SER 549 is missing expected H atoms. Skipping. Residue VAL 590 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8263 (ttt90) REVERT: A 177 GLN cc_start: 0.6354 (pp30) cc_final: 0.6093 (pp30) REVERT: A 359 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8145 (pttm) REVERT: B 178 TRP cc_start: 0.7740 (m-10) cc_final: 0.7196 (m-10) REVERT: I 231 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7355 (mt-10) outliers start: 17 outliers final: 14 residues processed: 94 average time/residue: 0.8084 time to fit residues: 83.1364 Evaluate side-chains 99 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 353 THR Chi-restraints excluded: chain I residue 376 GLU Chi-restraints excluded: chain I residue 400 ASP Chi-restraints excluded: chain I residue 445 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 57 optimal weight: 0.0770 chunk 111 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.0070 chunk 26 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 208 ASN B 352 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.206988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.165894 restraints weight = 27388.833| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.18 r_work: 0.3901 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9039 Z= 0.093 Angle : 0.520 9.348 12284 Z= 0.263 Chirality : 0.039 0.140 1405 Planarity : 0.004 0.059 1582 Dihedral : 4.842 58.487 1229 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.77 % Allowed : 17.46 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.26), residues: 1109 helix: 0.63 (0.46), residues: 135 sheet: -1.79 (0.28), residues: 319 loop : -0.26 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 343 TYR 0.013 0.001 TYR A 288 PHE 0.021 0.001 PHE I 87 TRP 0.009 0.001 TRP B 178 HIS 0.004 0.001 HIS I 372 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 9026) covalent geometry : angle 0.51830 (12258) SS BOND : bond 0.00173 ( 13) SS BOND : angle 1.13851 ( 26) hydrogen bonds : bond 0.03752 ( 218) hydrogen bonds : angle 6.01324 ( 597) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5572.19 seconds wall clock time: 94 minutes 55.01 seconds (5695.01 seconds total)