Starting phenix.real_space_refine on Sat Sep 28 00:54:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsc_43493/09_2024/8vsc_43493.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsc_43493/09_2024/8vsc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsc_43493/09_2024/8vsc_43493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsc_43493/09_2024/8vsc_43493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsc_43493/09_2024/8vsc_43493.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsc_43493/09_2024/8vsc_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-5461/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: 9.27, per 1000 atoms: 0.53 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: 4.44 Conformation dependent library (CDL) restraints added in 1.5 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: 1.94 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: 6.38 Time building geometry restraints manager: 5.31 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: 3.970 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: 0.290 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 40.550 Find NCS groups from input model: 0.310 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:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.730 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 1.518 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: 1.8519 time to fit residues: 176.0584 Evaluate side-chains 79 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 1.484 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8566 (ttt-90) REVERT: A 338 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8113 (p) REVERT: B 263 ASN cc_start: 0.7179 (p0) cc_final: 0.6936 (p0) REVERT: I 231 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: I 475 SER cc_start: 0.7490 (OUTLIER) cc_final: 0.7245 (m) outliers start: 24 outliers final: 9 residues processed: 100 average time/residue: 2.1093 time to fit residues: 229.4988 Evaluate side-chains 88 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 57 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 111 optimal weight: 0.0570 chunk 91 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9026 Z= 0.204 Angle : 0.565 5.021 12258 Z= 0.290 Chirality : 0.040 0.158 1405 Planarity : 0.005 0.064 1582 Dihedral : 5.734 70.437 1232 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.81 % Allowed : 12.79 % 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: -1.21 (0.25), residues: 1109 helix: 0.23 (0.44), residues: 135 sheet: -1.78 (0.27), residues: 314 loop : -0.40 (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 A 283 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 114 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8539 (ttt-90) REVERT: A 97 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7252 (tm130) REVERT: A 338 VAL cc_start: 0.8412 (OUTLIER) cc_final: 0.8082 (p) REVERT: B 263 ASN cc_start: 0.7119 (p0) cc_final: 0.6887 (p0) REVERT: I 231 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: I 510 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8071 (tt) outliers start: 27 outliers final: 11 residues processed: 103 average time/residue: 1.8152 time to fit residues: 205.9947 Evaluate side-chains 95 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 149 SER 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 101 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 0.0040 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.1998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9026 Z= 0.286 Angle : 0.587 5.956 12258 Z= 0.301 Chirality : 0.041 0.160 1405 Planarity : 0.004 0.042 1582 Dihedral : 5.752 70.548 1231 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.91 % Allowed : 13.83 % Favored : 83.26 % 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: -1.31 (0.25), residues: 1109 helix: 0.23 (0.44), residues: 136 sheet: -1.77 (0.28), residues: 304 loop : -0.57 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 281 HIS 0.004 0.001 HIS B 193 PHE 0.015 0.002 PHE B 188 TYR 0.017 0.002 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 108 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 80 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8551 (ttt-90) REVERT: A 97 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7280 (tm130) REVERT: A 177 GLN cc_start: 0.6852 (pp30) cc_final: 0.6559 (pp30) REVERT: A 338 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8186 (p) REVERT: B 178 TRP cc_start: 0.7720 (m-10) cc_final: 0.7308 (m-10) REVERT: B 263 ASN cc_start: 0.7175 (p0) cc_final: 0.6963 (p0) REVERT: I 475 SER cc_start: 0.7398 (OUTLIER) cc_final: 0.7114 (m) REVERT: I 510 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8124 (tt) outliers start: 28 outliers final: 12 residues processed: 99 average time/residue: 2.0085 time to fit residues: 217.0893 Evaluate side-chains 94 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 149 SER 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 376 GLU Chi-restraints excluded: chain I residue 380 LEU Chi-restraints excluded: chain I residue 445 LEU Chi-restraints excluded: chain I residue 475 SER 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 62 optimal weight: 0.0970 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 0.0870 chunk 45 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 overall best weight: 0.5356 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9026 Z= 0.174 Angle : 0.539 5.628 12258 Z= 0.275 Chirality : 0.039 0.155 1405 Planarity : 0.004 0.042 1582 Dihedral : 5.464 68.307 1231 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.29 % Allowed : 14.35 % 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: -1.16 (0.25), residues: 1109 helix: 0.44 (0.45), residues: 136 sheet: -1.84 (0.28), residues: 314 loop : -0.36 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 247 HIS 0.003 0.001 HIS I 372 PHE 0.012 0.001 PHE B 188 TYR 0.012 0.001 TYR A 142 ARG 0.005 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 110 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8521 (ttt-90) REVERT: A 130 ARG cc_start: 0.7363 (ttp-110) cc_final: 0.7055 (ttp80) REVERT: A 177 GLN cc_start: 0.6811 (pp30) cc_final: 0.6570 (pp30) REVERT: B 29 ARG cc_start: 0.7814 (mmt90) cc_final: 0.7562 (mtt180) REVERT: B 178 TRP cc_start: 0.7647 (m-10) cc_final: 0.7237 (m-10) REVERT: I 231 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7329 (mt-10) outliers start: 22 outliers final: 14 residues processed: 100 average time/residue: 1.9277 time to fit residues: 210.8250 Evaluate side-chains 98 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 190 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 380 LEU Chi-restraints excluded: chain I residue 400 ASP Chi-restraints excluded: chain I residue 445 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 90 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 0.0050 chunk 57 optimal weight: 0.0870 chunk 105 optimal weight: 3.9990 overall best weight: 0.5712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 137 GLN B 100 HIS B 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9026 Z= 0.184 Angle : 0.535 6.044 12258 Z= 0.272 Chirality : 0.039 0.154 1405 Planarity : 0.004 0.040 1582 Dihedral : 5.199 66.584 1229 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.39 % Allowed : 15.28 % 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: -1.15 (0.25), residues: 1109 helix: 0.52 (0.46), residues: 136 sheet: -1.86 (0.28), residues: 315 loop : -0.35 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 281 HIS 0.003 0.001 HIS I 372 PHE 0.013 0.001 PHE B 188 TYR 0.026 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 107 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 2.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8544 (ttt-90) REVERT: A 130 ARG cc_start: 0.7365 (ttp-110) cc_final: 0.7092 (ttm110) REVERT: A 177 GLN cc_start: 0.6807 (pp30) cc_final: 0.6568 (pp30) REVERT: B 29 ARG cc_start: 0.7803 (mmt90) cc_final: 0.7555 (mtt180) REVERT: B 178 TRP cc_start: 0.7566 (m-10) cc_final: 0.7163 (m-10) REVERT: I 231 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7334 (mt-10) outliers start: 23 outliers final: 14 residues processed: 98 average time/residue: 2.1059 time to fit residues: 225.8742 Evaluate side-chains 97 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1789 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= 0.272 Angle : 0.580 7.244 12258 Z= 0.293 Chirality : 0.041 0.157 1405 Planarity : 0.004 0.040 1582 Dihedral : 5.320 66.220 1229 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.49 % Allowed : 15.49 % Favored : 82.02 % 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: -1.26 (0.25), residues: 1109 helix: 0.45 (0.45), residues: 136 sheet: -1.84 (0.28), residues: 305 loop : -0.53 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 281 HIS 0.004 0.001 HIS I 181 PHE 0.015 0.002 PHE B 188 TYR 0.017 0.002 TYR B 103 ARG 0.009 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 105 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8329 (ttt90) REVERT: A 177 GLN cc_start: 0.6855 (pp30) cc_final: 0.6557 (pp30) REVERT: B 29 ARG cc_start: 0.7807 (mmt90) cc_final: 0.7602 (mtt180) REVERT: I 231 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7363 (mt-10) outliers start: 24 outliers final: 15 residues processed: 97 average time/residue: 2.0162 time to fit residues: 213.9766 Evaluate side-chains 91 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1877 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= 0.210 Angle : 0.554 7.368 12258 Z= 0.280 Chirality : 0.040 0.154 1405 Planarity : 0.004 0.044 1582 Dihedral : 5.210 64.625 1229 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.29 % Allowed : 16.22 % Favored : 81.50 % 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: -1.21 (0.25), residues: 1109 helix: 0.50 (0.46), residues: 136 sheet: -1.86 (0.28), residues: 305 loop : -0.45 (0.25), residues: 668 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 0.018 0.001 PHE I 87 TYR 0.017 0.002 TYR A 288 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 101 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8462 (ttt-90) REVERT: A 130 ARG cc_start: 0.7409 (ttp-110) cc_final: 0.7015 (ttm110) REVERT: A 177 GLN cc_start: 0.6821 (pp30) cc_final: 0.6575 (pp30) REVERT: I 231 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7330 (mt-10) outliers start: 22 outliers final: 15 residues processed: 92 average time/residue: 1.9924 time to fit residues: 200.2685 Evaluate side-chains 96 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 101 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 107 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9026 Z= 0.245 Angle : 0.565 8.803 12258 Z= 0.285 Chirality : 0.040 0.144 1405 Planarity : 0.005 0.086 1582 Dihedral : 5.232 63.801 1229 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.18 % Allowed : 16.42 % 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 (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: -1.23 (0.25), residues: 1109 helix: 0.49 (0.46), residues: 136 sheet: -1.86 (0.28), residues: 305 loop : -0.49 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 178 HIS 0.003 0.001 HIS I 181 PHE 0.014 0.001 PHE B 188 TYR 0.014 0.002 TYR A 142 ARG 0.016 0.001 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 105 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8477 (ttt-90) REVERT: A 177 GLN cc_start: 0.6821 (pp30) cc_final: 0.6518 (pp30) REVERT: A 359 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8142 (pttm) REVERT: I 231 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7357 (mt-10) outliers start: 21 outliers final: 14 residues processed: 97 average time/residue: 1.9327 time to fit residues: 205.2745 Evaluate side-chains 96 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 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 0.036 9026 Z= 0.199 Angle : 0.553 10.927 12258 Z= 0.278 Chirality : 0.040 0.138 1405 Planarity : 0.004 0.042 1582 Dihedral : 5.099 61.352 1229 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.08 % Allowed : 16.74 % 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 (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 (0.26), residues: 1109 helix: 0.59 (0.46), residues: 135 sheet: -1.81 (0.29), residues: 307 loop : -0.42 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 178 HIS 0.003 0.001 HIS I 372 PHE 0.012 0.001 PHE B 188 TYR 0.014 0.001 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 103 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8401 (ttt90) REVERT: A 177 GLN cc_start: 0.6784 (pp30) cc_final: 0.6491 (pp30) REVERT: A 359 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8185 (pttm) REVERT: B 178 TRP cc_start: 0.7624 (m-10) cc_final: 0.7011 (m-10) REVERT: I 231 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: I 475 SER cc_start: 0.7313 (OUTLIER) cc_final: 0.7090 (m) outliers start: 20 outliers final: 14 residues processed: 96 average time/residue: 1.8641 time to fit residues: 197.3975 Evaluate side-chains 98 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain I residue 475 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 89 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 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 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.204870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.163176 restraints weight = 27470.233| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.19 r_work: 0.3864 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2093 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= 0.213 Angle : 0.555 10.696 12258 Z= 0.279 Chirality : 0.040 0.141 1405 Planarity : 0.004 0.056 1582 Dihedral : 5.074 61.198 1229 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.08 % Allowed : 17.15 % 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 (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: -1.14 (0.26), residues: 1109 helix: 0.62 (0.46), residues: 135 sheet: -1.80 (0.29), residues: 307 loop : -0.43 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 178 HIS 0.003 0.001 HIS I 372 PHE 0.022 0.001 PHE I 87 TYR 0.014 0.002 TYR A 288 ARG 0.009 0.000 ARG A 343 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6003.92 seconds wall clock time: 104 minutes 19.37 seconds (6259.37 seconds total)