Starting phenix.real_space_refine on Wed Jan 22 00:51:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vsc_43493/01_2025/8vsc_43493.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vsc_43493/01_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_43493/01_2025/8vsc_43493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vsc_43493/01_2025/8vsc_43493.map" model { file = "/net/cci-nas-00/data/ceres_data/8vsc_43493/01_2025/8vsc_43493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vsc_43493/01_2025/8vsc_43493.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.055 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 3, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 8.90, per 1000 atoms: 0.50 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: 4.26 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.39 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: 6.34 Time building geometry restraints manager: 5.19 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: 3.070 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: 0.310 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 38.600 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.150 ------------------------------------------------------------------------------- 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 9026 Z= 0.238 Angle : 0.734 12.470 12258 Z= 0.393 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (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 TRP 0.009 0.001 TRP I 247 HIS 0.003 0.001 HIS A 283 PHE 0.014 0.001 PHE B 95 TYR 0.015 0.001 TYR A 142 ARG 0.018 0.001 ARG A 343 *********************** 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 : 1.345 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: 1.8048 time to fit residues: 171.4824 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 : 1.505 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.206923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.165432 restraints weight = 27821.898| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.13 r_work: 0.3875 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9026 Z= 0.275 Angle : 0.612 6.410 12258 Z= 0.316 Chirality : 0.041 0.170 1405 Planarity : 0.005 0.053 1582 Dihedral : 6.058 72.486 1236 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.49 % Allowed : 12.58 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 1109 helix: -0.06 (0.43), residues: 135 sheet: -1.66 (0.27), residues: 318 loop : -0.44 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 281 HIS 0.003 0.001 HIS I 106 PHE 0.016 0.002 PHE B 188 TYR 0.018 0.002 TYR A 142 ARG 0.004 0.000 ARG A 343 *********************** 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 108 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8433 (ttt-90) REVERT: A 338 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8052 (p) REVERT: B 263 ASN cc_start: 0.7159 (p0) cc_final: 0.6902 (p0) REVERT: I 231 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7310 (mt-10) REVERT: I 475 SER cc_start: 0.7743 (OUTLIER) cc_final: 0.7526 (m) outliers start: 24 outliers final: 9 residues processed: 100 average time/residue: 2.2169 time to fit residues: 241.0223 Evaluate side-chains 88 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 B residue 186 GLU 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 475 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 1 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.207448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.165785 restraints weight = 27528.149| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.14 r_work: 0.3883 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9026 Z= 0.206 Angle : 0.570 5.146 12258 Z= 0.292 Chirality : 0.040 0.160 1405 Planarity : 0.004 0.059 1582 Dihedral : 5.757 70.714 1232 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.60 % Allowed : 12.99 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.25), residues: 1109 helix: 0.20 (0.44), residues: 135 sheet: -1.78 (0.27), residues: 314 loop : -0.42 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 281 HIS 0.003 0.001 HIS I 372 PHE 0.013 0.001 PHE B 188 TYR 0.015 0.001 TYR A 142 ARG 0.008 0.000 ARG A 343 *********************** 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: 25 poor density : 86 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8322 (ttt-90) REVERT: A 97 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7134 (tm130) REVERT: A 338 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8032 (p) REVERT: B 263 ASN cc_start: 0.7060 (p0) cc_final: 0.6807 (p0) REVERT: I 231 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: I 510 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8089 (tt) outliers start: 25 outliers final: 10 residues processed: 100 average time/residue: 1.9208 time to fit residues: 211.2703 Evaluate side-chains 94 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 338 VAL 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 380 LEU Chi-restraints excluded: chain I residue 400 ASP 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 45 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 97 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4482 r_free = 0.4482 target = 0.206947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.165561 restraints weight = 27750.971| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.14 r_work: 0.3883 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9026 Z= 0.205 Angle : 0.551 5.665 12258 Z= 0.282 Chirality : 0.040 0.157 1405 Planarity : 0.004 0.041 1582 Dihedral : 5.542 68.698 1231 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.29 % Allowed : 14.03 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.25), residues: 1109 helix: 0.34 (0.45), residues: 136 sheet: -1.77 (0.28), residues: 314 loop : -0.36 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 281 HIS 0.003 0.001 HIS A 283 PHE 0.014 0.001 PHE B 188 TYR 0.014 0.001 TYR A 142 ARG 0.004 0.000 ARG A 16 *********************** 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 103 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8404 (ttt-90) REVERT: A 97 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.7142 (tm130) REVERT: A 177 GLN cc_start: 0.6416 (pp30) cc_final: 0.6090 (pp30) REVERT: B 178 TRP cc_start: 0.7912 (m-10) cc_final: 0.7463 (m-10) REVERT: B 263 ASN cc_start: 0.7147 (p0) cc_final: 0.6920 (p0) REVERT: I 510 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8125 (tt) outliers start: 22 outliers final: 10 residues processed: 94 average time/residue: 1.9128 time to fit residues: 197.6620 Evaluate side-chains 91 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 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 376 GLU Chi-restraints excluded: chain I residue 380 LEU 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 58 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 0.0980 chunk 98 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.205224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.164099 restraints weight = 27973.040| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.13 r_work: 0.3856 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9026 Z= 0.253 Angle : 0.566 6.922 12258 Z= 0.288 Chirality : 0.040 0.157 1405 Planarity : 0.004 0.041 1582 Dihedral : 5.393 68.245 1229 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.01 % Allowed : 13.62 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 1109 helix: 0.35 (0.45), residues: 136 sheet: -1.84 (0.28), residues: 314 loop : -0.46 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 281 HIS 0.003 0.001 HIS I 106 PHE 0.014 0.002 PHE I 87 TYR 0.015 0.002 TYR A 142 ARG 0.006 0.000 ARG A 343 *********************** 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 116 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8433 (ttt-90) REVERT: A 97 GLN cc_start: 0.7410 (pp30) cc_final: 0.7174 (tm130) REVERT: A 177 GLN cc_start: 0.6395 (pp30) cc_final: 0.6075 (pp30) REVERT: A 338 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8119 (p) REVERT: B 29 ARG cc_start: 0.7722 (mmt90) cc_final: 0.7501 (mtt180) REVERT: B 178 TRP cc_start: 0.7879 (m-10) cc_final: 0.7430 (m-10) REVERT: B 263 ASN cc_start: 0.7139 (p0) cc_final: 0.6909 (p0) REVERT: I 231 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: I 510 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8082 (tt) outliers start: 29 outliers final: 18 residues processed: 107 average time/residue: 2.0378 time to fit residues: 239.0671 Evaluate side-chains 103 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 149 SER Chi-restraints excluded: chain B residue 153 LEU 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 510 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 55 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 0.0070 chunk 111 optimal weight: 0.0670 chunk 76 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 overall best weight: 0.2536 ------------------------------------------------------------------------------- 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 = 0.4491 r_free = 0.4491 target = 0.208370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.167205 restraints weight = 27587.716| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.16 r_work: 0.3901 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9026 Z= 0.141 Angle : 0.520 5.798 12258 Z= 0.265 Chirality : 0.039 0.151 1405 Planarity : 0.004 0.046 1582 Dihedral : 5.064 64.566 1229 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.29 % Allowed : 15.18 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.26), residues: 1109 helix: 0.56 (0.46), residues: 136 sheet: -1.85 (0.29), residues: 299 loop : -0.24 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 247 HIS 0.004 0.001 HIS I 372 PHE 0.015 0.001 PHE B 95 TYR 0.030 0.001 TYR B 103 ARG 0.006 0.000 ARG A 343 *********************** 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 110 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8240 (ttt90) REVERT: A 97 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: A 177 GLN cc_start: 0.6397 (pp30) cc_final: 0.6133 (pp30) REVERT: B 29 ARG cc_start: 0.7687 (mmt90) cc_final: 0.7483 (mtt180) REVERT: I 566 LEU cc_start: 0.7517 (tp) cc_final: 0.7311 (mp) outliers start: 22 outliers final: 12 residues processed: 98 average time/residue: 2.0940 time to fit residues: 224.1418 Evaluate side-chains 99 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 205 VAL Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 168 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 76 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4460 r_free = 0.4460 target = 0.205121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.163306 restraints weight = 27581.294| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.19 r_work: 0.3865 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9026 Z= 0.254 Angle : 0.555 6.875 12258 Z= 0.282 Chirality : 0.040 0.154 1405 Planarity : 0.004 0.057 1582 Dihedral : 5.184 63.776 1229 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.60 % Allowed : 15.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.25), residues: 1109 helix: 0.53 (0.46), residues: 136 sheet: -1.80 (0.28), residues: 305 loop : -0.43 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 281 HIS 0.004 0.001 HIS I 181 PHE 0.015 0.001 PHE B 188 TYR 0.014 0.002 TYR A 142 ARG 0.008 0.000 ARG A 343 *********************** 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 113 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8170 (ttt90) REVERT: A 177 GLN cc_start: 0.6349 (pp30) cc_final: 0.6085 (pp30) REVERT: I 231 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7421 (mt-10) outliers start: 25 outliers final: 16 residues processed: 102 average time/residue: 2.0157 time to fit residues: 224.8466 Evaluate side-chains 102 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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 205 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4446 r_free = 0.4446 target = 0.203616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.162477 restraints weight = 27673.838| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.12 r_work: 0.3847 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9026 Z= 0.277 Angle : 0.574 7.449 12258 Z= 0.291 Chirality : 0.041 0.155 1405 Planarity : 0.005 0.063 1582 Dihedral : 5.254 63.201 1229 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.18 % Allowed : 15.49 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 1109 helix: 0.45 (0.46), residues: 136 sheet: -1.84 (0.29), residues: 305 loop : -0.51 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 178 HIS 0.003 0.001 HIS I 181 PHE 0.020 0.002 PHE I 87 TYR 0.015 0.002 TYR A 142 ARG 0.008 0.000 ARG A 343 *********************** 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: 21 poor density : 84 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8188 (ttt90) REVERT: A 177 GLN cc_start: 0.6486 (pp30) cc_final: 0.6220 (pp30) REVERT: I 231 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7411 (mt-10) outliers start: 21 outliers final: 16 residues processed: 96 average time/residue: 1.9807 time to fit residues: 208.6890 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 : 1.422 ------------------------------------------------------------------------------- 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 205 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 13 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 57 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 82 optimal weight: 0.7980 chunk 88 optimal weight: 0.0980 chunk 49 optimal weight: 0.2980 overall best weight: 0.2380 ------------------------------------------------------------------------------- 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 = 0.4482 r_free = 0.4482 target = 0.207317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.166414 restraints weight = 27552.795| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.14 r_work: 0.3889 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9026 Z= 0.142 Angle : 0.528 10.053 12258 Z= 0.267 Chirality : 0.039 0.137 1405 Planarity : 0.005 0.108 1582 Dihedral : 4.982 59.542 1229 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.98 % Allowed : 16.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.25), residues: 1109 helix: 0.63 (0.47), residues: 136 sheet: -1.80 (0.29), residues: 305 loop : -0.34 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 178 HIS 0.004 0.001 HIS I 372 PHE 0.010 0.001 PHE B 188 TYR 0.021 0.001 TYR A 288 ARG 0.016 0.000 ARG A 123 *********************** 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 109 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8260 (ttt90) REVERT: A 177 GLN cc_start: 0.6474 (pp30) cc_final: 0.6207 (pp30) REVERT: A 229 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6248 (mm) REVERT: I 231 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7381 (mt-10) outliers start: 19 outliers final: 12 residues processed: 101 average time/residue: 2.0642 time to fit residues: 230.9478 Evaluate side-chains 100 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 229 LEU Chi-restraints excluded: chain A residue 289 HIS 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 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 55 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4457 r_free = 0.4457 target = 0.204781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.163677 restraints weight = 27674.189| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.12 r_work: 0.3860 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9026 Z= 0.239 Angle : 0.555 11.309 12258 Z= 0.280 Chirality : 0.040 0.141 1405 Planarity : 0.004 0.051 1582 Dihedral : 5.061 60.178 1229 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.66 % Allowed : 16.74 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.25), residues: 1109 helix: 0.59 (0.47), residues: 135 sheet: -1.77 (0.29), residues: 307 loop : -0.42 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 178 HIS 0.003 0.001 HIS A 283 PHE 0.014 0.001 PHE B 188 TYR 0.014 0.002 TYR A 288 ARG 0.010 0.000 ARG A 343 ********************** 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 101 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 1.527 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: 0.8771 (OUTLIER) cc_final: 0.8340 (ttt90) REVERT: A 177 GLN cc_start: 0.6463 (pp30) cc_final: 0.6197 (pp30) REVERT: A 229 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6324 (mm) REVERT: B 178 TRP cc_start: 0.7745 (m-10) cc_final: 0.7247 (m-10) REVERT: I 231 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7418 (mt-10) outliers start: 16 outliers final: 13 residues processed: 95 average time/residue: 1.9631 time to fit residues: 204.7162 Evaluate side-chains 101 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 229 LEU Chi-restraints excluded: chain A residue 289 HIS 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 99 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 104 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.0170 chunk 46 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.207183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.166023 restraints weight = 27652.451| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.14 r_work: 0.3883 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9026 Z= 0.160 Angle : 0.521 9.102 12258 Z= 0.263 Chirality : 0.039 0.138 1405 Planarity : 0.004 0.057 1582 Dihedral : 4.885 57.890 1229 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.66 % Allowed : 17.05 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.26), residues: 1109 helix: 0.64 (0.47), residues: 135 sheet: -1.81 (0.29), residues: 317 loop : -0.28 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 178 HIS 0.004 0.001 HIS I 372 PHE 0.022 0.001 PHE I 87 TYR 0.015 0.001 TYR A 288 ARG 0.010 0.000 ARG A 343 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11604.82 seconds wall clock time: 203 minutes 54.41 seconds (12234.41 seconds total)