Starting phenix.real_space_refine on Fri Jul 19 18:17:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jio_36322/07_2024/8jio_36322.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jio_36322/07_2024/8jio_36322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jio_36322/07_2024/8jio_36322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jio_36322/07_2024/8jio_36322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jio_36322/07_2024/8jio_36322.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jio_36322/07_2024/8jio_36322.cif" } resolution = 3.3 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 5524 2.51 5 N 1452 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8698 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5350 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 35, 'TRANS': 641} Chain: "B" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "C" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1713 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 14, 'TRANS': 214} Time building chain proxies: 5.14, per 1000 atoms: 0.59 Number of scatterers: 8698 At special positions: 0 Unit cell: (117.432, 91.336, 152.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1688 8.00 N 1452 7.00 C 5524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 205 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.25 Conformation dependent library (CDL) restraints added in 1.8 seconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 23 sheets defined 4.3% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.839A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.540A pdb=" N ASN A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.862A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.789A pdb=" N LYS B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.732A pdb=" N GLU B 187 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.520A pdb=" N THR C 90 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.661A pdb=" N LEU A 277 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 273 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN A 271 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 71 removed outlier: 4.096A pdb=" N HIS A 70 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 78 " --> pdb=" O HIS A 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.811A pdb=" N SER A 117 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 106 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 239 " --> pdb=" O TRP A 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 191 removed outlier: 3.940A pdb=" N LYS A 187 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 189 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 202 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.693A pdb=" N VAL A 597 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASN A 641 " --> pdb=" O GLY A 652 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.623A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 435 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.169A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 550 through 554 Processing sheet with id=AB2, first strand: chain 'A' and resid 655 through 659 removed outlier: 4.537A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AB4, first strand: chain 'B' and resid 19 through 23 removed outlier: 3.513A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 34 through 37 removed outlier: 6.751A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB7, first strand: chain 'B' and resid 130 through 139 removed outlier: 3.526A pdb=" N ALA B 130 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 132 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 176 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 145 through 149 removed outlier: 3.701A pdb=" N LYS B 145 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR B 197 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.533A pdb=" N GLN C 5 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS C 22 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE C 78 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.676A pdb=" N ALA C 91 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP C 98 " --> pdb=" O TYR C 33 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 49 through 51 Processing sheet with id=AC3, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.629A pdb=" N GLY C 148 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS C 149 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER C 189 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C 190 " --> pdb=" O HIS C 173 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.629A pdb=" N GLY C 148 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS C 152 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU C 187 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR C 154 " --> pdb=" O TYR C 185 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL C 178 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 162 through 163 141 hydrogen bonds defined for protein. 336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2770 1.34 - 1.46: 2142 1.46 - 1.58: 3969 1.58 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 8920 Sorted by residual: bond pdb=" N ILE A 584 " pdb=" CA ILE A 584 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.58e+00 bond pdb=" N LEU A 582 " pdb=" CA LEU A 582 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.31e-02 5.83e+03 6.39e+00 bond pdb=" N GLU A 583 " pdb=" CA GLU A 583 " ideal model delta sigma weight residual 1.461 1.487 -0.026 1.20e-02 6.94e+03 4.73e+00 bond pdb=" N THR A 581 " pdb=" CA THR A 581 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.27e-02 6.20e+03 4.60e+00 bond pdb=" C TYR A 39 " pdb=" N PRO A 40 " ideal model delta sigma weight residual 1.326 1.353 -0.027 1.44e-02 4.82e+03 3.53e+00 ... (remaining 8915 not shown) Histogram of bond angle deviations from ideal: 100.79 - 107.43: 332 107.43 - 114.07: 4964 114.07 - 120.71: 3272 120.71 - 127.35: 3493 127.35 - 133.99: 88 Bond angle restraints: 12149 Sorted by residual: angle pdb=" N TYR A 351 " pdb=" CA TYR A 351 " pdb=" C TYR A 351 " ideal model delta sigma weight residual 114.75 107.35 7.40 1.26e+00 6.30e-01 3.45e+01 angle pdb=" N VAL A 503 " pdb=" CA VAL A 503 " pdb=" C VAL A 503 " ideal model delta sigma weight residual 113.47 109.28 4.19 1.01e+00 9.80e-01 1.72e+01 angle pdb=" C LEU A 582 " pdb=" CA LEU A 582 " pdb=" CB LEU A 582 " ideal model delta sigma weight residual 109.84 116.04 -6.20 1.50e+00 4.44e-01 1.71e+01 angle pdb=" CA TYR A 351 " pdb=" C TYR A 351 " pdb=" N ALA A 352 " ideal model delta sigma weight residual 119.80 115.46 4.34 1.34e+00 5.57e-01 1.05e+01 angle pdb=" N VAL A 350 " pdb=" CA VAL A 350 " pdb=" C VAL A 350 " ideal model delta sigma weight residual 106.21 109.52 -3.31 1.07e+00 8.73e-01 9.57e+00 ... (remaining 12144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.09: 5019 14.09 - 28.19: 198 28.19 - 42.28: 52 42.28 - 56.38: 11 56.38 - 70.47: 6 Dihedral angle restraints: 5286 sinusoidal: 2026 harmonic: 3260 Sorted by residual: dihedral pdb=" CA VAL A 350 " pdb=" C VAL A 350 " pdb=" N TYR A 351 " pdb=" CA TYR A 351 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -115.75 29.75 1 1.00e+01 1.00e-02 1.27e+01 dihedral pdb=" C LEU A 582 " pdb=" N LEU A 582 " pdb=" CA LEU A 582 " pdb=" CB LEU A 582 " ideal model delta harmonic sigma weight residual -122.60 -130.40 7.80 0 2.50e+00 1.60e-01 9.75e+00 ... (remaining 5283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1206 0.075 - 0.151: 145 0.151 - 0.226: 3 0.226 - 0.302: 0 0.302 - 0.377: 1 Chirality restraints: 1355 Sorted by residual: chirality pdb=" CG LEU A 582 " pdb=" CB LEU A 582 " pdb=" CD1 LEU A 582 " pdb=" CD2 LEU A 582 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA ILE A 584 " pdb=" N ILE A 584 " pdb=" C ILE A 584 " pdb=" CB ILE A 584 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LEU A 582 " pdb=" N LEU A 582 " pdb=" C LEU A 582 " pdb=" CB LEU A 582 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 1352 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 140 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.12e+00 pdb=" N PRO B 141 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 79 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.25e+00 pdb=" N PRO B 80 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 127 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO C 128 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 128 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 128 " 0.027 5.00e-02 4.00e+02 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 905 2.76 - 3.29: 8112 3.29 - 3.83: 13606 3.83 - 4.36: 15743 4.36 - 4.90: 26733 Nonbonded interactions: 65099 Sorted by model distance: nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.220 2.440 nonbonded pdb=" OE1 GLU A 340 " pdb=" OG SER B 56 " model vdw 2.259 2.440 nonbonded pdb=" O TYR B 49 " pdb=" OG1 THR B 53 " model vdw 2.270 2.440 nonbonded pdb=" OG SER A 469 " pdb=" OE1 GLU A 471 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR B 36 " pdb=" NE2 GLN B 89 " model vdw 2.283 2.520 ... (remaining 65094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.760 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8920 Z= 0.138 Angle : 0.520 7.403 12149 Z= 0.310 Chirality : 0.044 0.377 1355 Planarity : 0.004 0.062 1563 Dihedral : 8.535 70.474 3175 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.53 % Favored : 91.38 % Rotamer: Outliers : 3.78 % Allowed : 5.82 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.63 (0.21), residues: 1114 helix: -4.23 (0.38), residues: 30 sheet: -2.90 (0.29), residues: 257 loop : -3.35 (0.18), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 36 HIS 0.001 0.000 HIS A 625 PHE 0.005 0.001 PHE B 139 TYR 0.005 0.001 TYR C 53 ARG 0.003 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 279 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 VAL cc_start: 0.1587 (OUTLIER) cc_final: 0.1300 (m) REVERT: A 55 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6348 (mt) REVERT: A 60 PHE cc_start: 0.6994 (m-80) cc_final: 0.6412 (m-80) REVERT: A 82 ASN cc_start: 0.6932 (m-40) cc_final: 0.6524 (m-40) REVERT: A 274 THR cc_start: 0.6818 (p) cc_final: 0.6563 (p) REVERT: A 298 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6657 (mt-10) REVERT: A 378 LYS cc_start: 0.7706 (pttm) cc_final: 0.7391 (pttm) REVERT: A 396 TYR cc_start: 0.8387 (m-80) cc_final: 0.7979 (m-10) REVERT: A 406 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7391 (mt-10) REVERT: A 422 ASN cc_start: 0.7320 (m-40) cc_final: 0.7115 (m110) REVERT: A 442 ASP cc_start: 0.6840 (m-30) cc_final: 0.6537 (m-30) REVERT: A 472 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.6009 (pt) REVERT: A 547 THR cc_start: 0.7861 (m) cc_final: 0.7598 (p) REVERT: A 556 ASN cc_start: 0.7664 (m-40) cc_final: 0.7310 (m-40) REVERT: A 573 THR cc_start: 0.8783 (m) cc_final: 0.8521 (p) REVERT: A 578 ASP cc_start: 0.7042 (m-30) cc_final: 0.6599 (m-30) REVERT: A 581 THR cc_start: 0.8308 (p) cc_final: 0.7930 (p) REVERT: A 583 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6253 (mt-10) REVERT: A 584 ILE cc_start: 0.4816 (OUTLIER) cc_final: 0.4556 (pt) REVERT: A 612 TYR cc_start: 0.7081 (m-80) cc_final: 0.6253 (m-80) REVERT: A 624 ILE cc_start: 0.6733 (OUTLIER) cc_final: 0.6481 (pt) REVERT: A 643 PHE cc_start: 0.5231 (m-80) cc_final: 0.4791 (m-80) REVERT: A 645 THR cc_start: 0.6690 (p) cc_final: 0.6006 (t) REVERT: B 107 LYS cc_start: 0.8417 (mtmp) cc_final: 0.8151 (ptpp) REVERT: B 108 ARG cc_start: 0.7005 (mmt90) cc_final: 0.6664 (mmt90) REVERT: B 123 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 148 TRP cc_start: 0.5480 (OUTLIER) cc_final: 0.5203 (m100) REVERT: B 177 SER cc_start: 0.7074 (m) cc_final: 0.6568 (p) REVERT: B 179 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6025 (tm) REVERT: B 181 LEU cc_start: 0.8347 (mt) cc_final: 0.7802 (mt) REVERT: C 75 LYS cc_start: 0.8650 (ptmt) cc_final: 0.7850 (ptpp) REVERT: C 78 PHE cc_start: 0.7710 (p90) cc_final: 0.7452 (p90) REVERT: C 84 SER cc_start: 0.7689 (p) cc_final: 0.7172 (p) REVERT: C 92 VAL cc_start: 0.8236 (t) cc_final: 0.7682 (p) REVERT: C 179 LEU cc_start: 0.7936 (mt) cc_final: 0.7718 (mt) REVERT: C 220 VAL cc_start: 0.7528 (t) cc_final: 0.6972 (p) outliers start: 37 outliers final: 17 residues processed: 300 average time/residue: 0.2119 time to fit residues: 84.8750 Evaluate side-chains 253 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 228 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 149 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 62 ASN ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN A 135 GLN A 185 ASN A 280 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 625 HIS A 641 ASN B 6 GLN B 27 GLN B 38 GLN B 89 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN C 58 ASN ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 8920 Z= 0.332 Angle : 0.671 9.325 12149 Z= 0.341 Chirality : 0.047 0.188 1355 Planarity : 0.006 0.061 1563 Dihedral : 7.353 82.792 1262 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.58 % Favored : 88.33 % Rotamer: Outliers : 5.62 % Allowed : 12.26 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.13 (0.22), residues: 1114 helix: -4.04 (0.38), residues: 43 sheet: -2.27 (0.28), residues: 303 loop : -3.06 (0.19), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 34 HIS 0.004 0.001 HIS A 339 PHE 0.019 0.002 PHE A 275 TYR 0.019 0.002 TYR A 313 ARG 0.011 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 254 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6770 (mt) REVERT: A 60 PHE cc_start: 0.7128 (m-80) cc_final: 0.6450 (m-80) REVERT: A 202 LYS cc_start: 0.5638 (mttt) cc_final: 0.4860 (mtmt) REVERT: A 273 ARG cc_start: 0.6828 (mtt180) cc_final: 0.6537 (mtt180) REVERT: A 320 VAL cc_start: 0.7762 (m) cc_final: 0.7011 (p) REVERT: A 382 VAL cc_start: 0.8336 (t) cc_final: 0.7982 (p) REVERT: A 392 PHE cc_start: 0.7298 (m-80) cc_final: 0.6889 (m-80) REVERT: A 434 ILE cc_start: 0.8481 (mp) cc_final: 0.8183 (mt) REVERT: A 487 ASN cc_start: 0.7606 (m-40) cc_final: 0.7321 (m-40) REVERT: A 556 ASN cc_start: 0.7802 (m-40) cc_final: 0.7525 (m-40) REVERT: A 562 PHE cc_start: 0.7181 (m-10) cc_final: 0.6785 (m-80) REVERT: A 565 PHE cc_start: 0.6549 (t80) cc_final: 0.6326 (t80) REVERT: A 578 ASP cc_start: 0.7297 (m-30) cc_final: 0.6666 (m-30) REVERT: A 583 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6371 (mt-10) REVERT: A 584 ILE cc_start: 0.5213 (OUTLIER) cc_final: 0.4842 (pt) REVERT: A 612 TYR cc_start: 0.7260 (m-80) cc_final: 0.6171 (m-80) REVERT: A 624 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6633 (pt) REVERT: A 643 PHE cc_start: 0.5066 (m-80) cc_final: 0.4811 (m-80) REVERT: B 24 ARG cc_start: 0.7176 (mtp-110) cc_final: 0.6833 (mtp85) REVERT: B 108 ARG cc_start: 0.7167 (mmt90) cc_final: 0.6815 (mmt90) REVERT: B 123 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7864 (mt-10) REVERT: B 142 ARG cc_start: 0.7608 (ptp90) cc_final: 0.7146 (ptp90) REVERT: B 147 GLN cc_start: 0.6213 (tm-30) cc_final: 0.5996 (tm-30) REVERT: B 177 SER cc_start: 0.7564 (m) cc_final: 0.7208 (p) REVERT: C 54 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8182 (t) REVERT: C 75 LYS cc_start: 0.8805 (ptmt) cc_final: 0.8172 (ptpp) REVERT: C 78 PHE cc_start: 0.8183 (p90) cc_final: 0.7956 (p90) REVERT: C 92 VAL cc_start: 0.8294 (t) cc_final: 0.7975 (p) outliers start: 55 outliers final: 30 residues processed: 279 average time/residue: 0.2166 time to fit residues: 81.4406 Evaluate side-chains 275 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 241 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 206 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 0.0870 chunk 80 optimal weight: 5.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 8920 Z= 0.260 Angle : 0.634 9.488 12149 Z= 0.317 Chirality : 0.046 0.161 1355 Planarity : 0.005 0.063 1563 Dihedral : 6.434 59.840 1249 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.32 % Favored : 89.59 % Rotamer: Outliers : 5.52 % Allowed : 14.91 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.78 (0.22), residues: 1114 helix: -3.48 (0.57), residues: 37 sheet: -2.01 (0.29), residues: 291 loop : -2.86 (0.19), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 34 HIS 0.005 0.001 HIS A 67 PHE 0.017 0.002 PHE B 118 TYR 0.016 0.001 TYR C 50 ARG 0.006 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 247 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7466 (mt) cc_final: 0.6888 (mm) REVERT: A 60 PHE cc_start: 0.7005 (m-80) cc_final: 0.6365 (m-80) REVERT: A 320 VAL cc_start: 0.7464 (m) cc_final: 0.7201 (m) REVERT: A 349 SER cc_start: 0.8494 (m) cc_final: 0.8221 (m) REVERT: A 378 LYS cc_start: 0.7583 (pttm) cc_final: 0.7350 (pttm) REVERT: A 392 PHE cc_start: 0.7280 (m-80) cc_final: 0.6933 (m-80) REVERT: A 396 TYR cc_start: 0.8351 (m-80) cc_final: 0.8139 (m-10) REVERT: A 422 ASN cc_start: 0.7511 (m110) cc_final: 0.7243 (m110) REVERT: A 434 ILE cc_start: 0.8446 (mp) cc_final: 0.8124 (mt) REVERT: A 556 ASN cc_start: 0.7760 (m-40) cc_final: 0.7490 (m-40) REVERT: A 565 PHE cc_start: 0.6504 (t80) cc_final: 0.6229 (t80) REVERT: A 583 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6984 (mt-10) REVERT: A 612 TYR cc_start: 0.7354 (m-80) cc_final: 0.6245 (m-80) REVERT: A 624 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6907 (pt) REVERT: A 627 ASP cc_start: 0.5448 (p0) cc_final: 0.5143 (p0) REVERT: A 629 LEU cc_start: 0.7700 (mm) cc_final: 0.7124 (mt) REVERT: A 643 PHE cc_start: 0.4982 (m-80) cc_final: 0.4731 (m-80) REVERT: B 97 THR cc_start: 0.8544 (t) cc_final: 0.8326 (p) REVERT: B 106 ILE cc_start: 0.8475 (mp) cc_final: 0.8265 (mp) REVERT: B 108 ARG cc_start: 0.7129 (mmt90) cc_final: 0.6794 (mmt90) REVERT: B 142 ARG cc_start: 0.7541 (ptp90) cc_final: 0.7077 (ptp90) REVERT: B 147 GLN cc_start: 0.6238 (tm-30) cc_final: 0.5889 (tm-30) REVERT: B 177 SER cc_start: 0.7613 (m) cc_final: 0.7342 (p) REVERT: C 11 LEU cc_start: 0.7883 (mt) cc_final: 0.7646 (mt) REVERT: C 78 PHE cc_start: 0.8274 (p90) cc_final: 0.8040 (p90) REVERT: C 92 VAL cc_start: 0.8323 (t) cc_final: 0.8004 (p) REVERT: C 99 TYR cc_start: 0.8168 (t80) cc_final: 0.7934 (t80) outliers start: 54 outliers final: 36 residues processed: 271 average time/residue: 0.2298 time to fit residues: 82.6602 Evaluate side-chains 267 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 230 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 110 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8920 Z= 0.211 Angle : 0.632 12.718 12149 Z= 0.311 Chirality : 0.046 0.260 1355 Planarity : 0.005 0.062 1563 Dihedral : 6.115 55.795 1245 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.86 % Favored : 89.05 % Rotamer: Outliers : 5.01 % Allowed : 17.06 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.53 (0.23), residues: 1114 helix: -3.10 (0.68), residues: 37 sheet: -1.80 (0.30), residues: 290 loop : -2.71 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 34 HIS 0.003 0.000 HIS A 67 PHE 0.022 0.001 PHE A 497 TYR 0.018 0.001 TYR C 50 ARG 0.005 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 234 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.6906 (mm) REVERT: A 60 PHE cc_start: 0.6996 (m-80) cc_final: 0.6327 (m-80) REVERT: A 98 LYS cc_start: 0.7265 (mtmm) cc_final: 0.6942 (mppt) REVERT: A 266 TYR cc_start: 0.3325 (m-10) cc_final: 0.2448 (m-10) REVERT: A 320 VAL cc_start: 0.7441 (m) cc_final: 0.7166 (m) REVERT: A 349 SER cc_start: 0.8496 (m) cc_final: 0.8255 (m) REVERT: A 378 LYS cc_start: 0.7611 (pttm) cc_final: 0.7380 (pttm) REVERT: A 422 ASN cc_start: 0.7472 (m110) cc_final: 0.7165 (m110) REVERT: A 434 ILE cc_start: 0.8414 (mp) cc_final: 0.8121 (mt) REVERT: A 451 TYR cc_start: 0.8280 (m-10) cc_final: 0.7961 (m-80) REVERT: A 455 LEU cc_start: 0.8210 (tp) cc_final: 0.7996 (tt) REVERT: A 468 ILE cc_start: 0.8283 (mt) cc_final: 0.7990 (mt) REVERT: A 556 ASN cc_start: 0.7740 (m-40) cc_final: 0.7478 (m-40) REVERT: A 565 PHE cc_start: 0.6428 (t80) cc_final: 0.6151 (t80) REVERT: A 583 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7021 (mt-10) REVERT: A 587 ILE cc_start: 0.8748 (mt) cc_final: 0.8543 (mt) REVERT: A 612 TYR cc_start: 0.7369 (m-80) cc_final: 0.6267 (m-80) REVERT: A 624 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.7109 (pt) REVERT: A 627 ASP cc_start: 0.5014 (p0) cc_final: 0.4542 (p0) REVERT: A 643 PHE cc_start: 0.4943 (m-80) cc_final: 0.4626 (m-80) REVERT: B 24 ARG cc_start: 0.7336 (mtp-110) cc_final: 0.6947 (mtp85) REVERT: B 90 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7510 (tm-30) REVERT: B 97 THR cc_start: 0.8564 (t) cc_final: 0.8331 (p) REVERT: B 108 ARG cc_start: 0.7111 (mmt90) cc_final: 0.6812 (mmt90) REVERT: B 177 SER cc_start: 0.7598 (m) cc_final: 0.7368 (p) REVERT: C 45 LEU cc_start: 0.8541 (mm) cc_final: 0.8333 (mt) REVERT: C 75 LYS cc_start: 0.8597 (ptmt) cc_final: 0.8312 (ptpp) REVERT: C 92 VAL cc_start: 0.8310 (t) cc_final: 0.7991 (p) REVERT: C 99 TYR cc_start: 0.8128 (t80) cc_final: 0.7900 (t80) outliers start: 49 outliers final: 37 residues processed: 255 average time/residue: 0.2246 time to fit residues: 76.3700 Evaluate side-chains 270 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 231 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 206 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8920 Z= 0.263 Angle : 0.692 26.854 12149 Z= 0.344 Chirality : 0.048 0.358 1355 Planarity : 0.005 0.063 1563 Dihedral : 6.251 54.042 1244 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.21 % Favored : 87.61 % Rotamer: Outliers : 5.62 % Allowed : 17.57 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.42 (0.23), residues: 1114 helix: -3.25 (0.72), residues: 36 sheet: -1.80 (0.30), residues: 297 loop : -2.59 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 34 HIS 0.006 0.001 HIS A 67 PHE 0.026 0.001 PHE B 118 TYR 0.025 0.002 TYR C 50 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 244 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.7246 (mt0) cc_final: 0.6964 (mt0) REVERT: A 57 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.6961 (mm) REVERT: A 60 PHE cc_start: 0.6973 (m-80) cc_final: 0.6290 (m-80) REVERT: A 266 TYR cc_start: 0.3536 (m-10) cc_final: 0.2619 (m-10) REVERT: A 355 ARG cc_start: 0.7430 (ttm170) cc_final: 0.6894 (ttm170) REVERT: A 392 PHE cc_start: 0.7460 (m-80) cc_final: 0.7089 (m-80) REVERT: A 422 ASN cc_start: 0.7550 (m110) cc_final: 0.7205 (m110) REVERT: A 434 ILE cc_start: 0.8448 (mp) cc_final: 0.8139 (mt) REVERT: A 451 TYR cc_start: 0.8316 (m-10) cc_final: 0.7933 (m-80) REVERT: A 455 LEU cc_start: 0.8325 (tp) cc_final: 0.8067 (tt) REVERT: A 556 ASN cc_start: 0.7772 (m-40) cc_final: 0.7531 (m-40) REVERT: A 578 ASP cc_start: 0.7338 (m-30) cc_final: 0.6870 (m-30) REVERT: A 583 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6815 (mt-10) REVERT: A 587 ILE cc_start: 0.8778 (mt) cc_final: 0.8561 (mt) REVERT: A 612 TYR cc_start: 0.7487 (m-80) cc_final: 0.6355 (m-80) REVERT: A 627 ASP cc_start: 0.5379 (p0) cc_final: 0.4744 (p0) REVERT: A 629 LEU cc_start: 0.7711 (mm) cc_final: 0.7193 (mt) REVERT: B 54 LEU cc_start: 0.8199 (mp) cc_final: 0.7991 (mm) REVERT: B 97 THR cc_start: 0.8609 (t) cc_final: 0.8363 (p) REVERT: B 108 ARG cc_start: 0.7170 (mmt90) cc_final: 0.6879 (mmt90) REVERT: B 147 GLN cc_start: 0.6609 (tm-30) cc_final: 0.6117 (tm-30) REVERT: B 177 SER cc_start: 0.7687 (m) cc_final: 0.7427 (p) REVERT: C 75 LYS cc_start: 0.8727 (ptmt) cc_final: 0.8437 (ptpp) REVERT: C 77 GLN cc_start: 0.8301 (pt0) cc_final: 0.8093 (pt0) REVERT: C 99 TYR cc_start: 0.8127 (t80) cc_final: 0.7923 (t80) REVERT: C 133 LEU cc_start: 0.4906 (OUTLIER) cc_final: 0.4180 (pp) REVERT: C 187 LEU cc_start: 0.7686 (pp) cc_final: 0.7347 (pt) outliers start: 55 outliers final: 40 residues processed: 271 average time/residue: 0.2428 time to fit residues: 88.1340 Evaluate side-chains 273 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 231 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 206 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.0870 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.0670 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8920 Z= 0.198 Angle : 0.658 18.714 12149 Z= 0.326 Chirality : 0.047 0.336 1355 Planarity : 0.005 0.062 1563 Dihedral : 5.987 53.653 1241 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.68 % Favored : 89.23 % Rotamer: Outliers : 4.90 % Allowed : 19.41 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.26 (0.23), residues: 1114 helix: -3.27 (0.71), residues: 36 sheet: -1.69 (0.29), residues: 298 loop : -2.46 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 34 HIS 0.004 0.001 HIS A 67 PHE 0.020 0.001 PHE A 565 TYR 0.023 0.001 TYR C 50 ARG 0.007 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 235 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.7199 (mt0) cc_final: 0.6866 (mt0) REVERT: A 57 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.6949 (mm) REVERT: A 60 PHE cc_start: 0.6937 (m-80) cc_final: 0.6303 (m-80) REVERT: A 266 TYR cc_start: 0.3439 (m-10) cc_final: 0.2517 (m-10) REVERT: A 378 LYS cc_start: 0.7519 (pttm) cc_final: 0.7263 (pttm) REVERT: A 422 ASN cc_start: 0.7502 (m-40) cc_final: 0.7199 (m-40) REVERT: A 434 ILE cc_start: 0.8425 (mp) cc_final: 0.8071 (mt) REVERT: A 451 TYR cc_start: 0.8267 (m-10) cc_final: 0.7925 (m-80) REVERT: A 455 LEU cc_start: 0.8301 (tp) cc_final: 0.8055 (tt) REVERT: A 516 GLU cc_start: 0.7151 (tt0) cc_final: 0.6745 (tt0) REVERT: A 529 LYS cc_start: 0.7827 (mmmm) cc_final: 0.7391 (mmmm) REVERT: A 556 ASN cc_start: 0.7741 (m-40) cc_final: 0.7485 (m-40) REVERT: A 578 ASP cc_start: 0.7298 (m-30) cc_final: 0.6825 (m-30) REVERT: A 583 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6934 (mt-10) REVERT: A 587 ILE cc_start: 0.8785 (mt) cc_final: 0.8538 (mt) REVERT: A 612 TYR cc_start: 0.7439 (m-80) cc_final: 0.6322 (m-80) REVERT: A 627 ASP cc_start: 0.5262 (p0) cc_final: 0.5035 (p0) REVERT: A 629 LEU cc_start: 0.7593 (mm) cc_final: 0.7084 (mt) REVERT: B 9 SER cc_start: 0.7841 (m) cc_final: 0.7598 (p) REVERT: B 42 LYS cc_start: 0.8151 (mttp) cc_final: 0.7946 (mttp) REVERT: B 54 LEU cc_start: 0.8189 (mp) cc_final: 0.7977 (mm) REVERT: B 97 THR cc_start: 0.8612 (t) cc_final: 0.8372 (p) REVERT: B 108 ARG cc_start: 0.7149 (mmt90) cc_final: 0.6847 (mmt90) REVERT: B 142 ARG cc_start: 0.7518 (ptp90) cc_final: 0.7037 (ptp90) REVERT: C 38 ARG cc_start: 0.8407 (ttp-170) cc_final: 0.8136 (mtp180) outliers start: 48 outliers final: 41 residues processed: 259 average time/residue: 0.2379 time to fit residues: 81.1503 Evaluate side-chains 272 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 230 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 206 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 59 optimal weight: 0.0270 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8920 Z= 0.186 Angle : 0.650 19.565 12149 Z= 0.322 Chirality : 0.046 0.321 1355 Planarity : 0.005 0.061 1563 Dihedral : 5.953 53.521 1241 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.58 % Favored : 88.33 % Rotamer: Outliers : 5.52 % Allowed : 19.51 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.15 (0.23), residues: 1114 helix: -3.47 (0.66), residues: 36 sheet: -1.57 (0.29), residues: 284 loop : -2.38 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 34 HIS 0.003 0.001 HIS A 67 PHE 0.016 0.001 PHE B 118 TYR 0.022 0.001 TYR C 50 ARG 0.006 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 232 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.6956 (mm) REVERT: A 60 PHE cc_start: 0.6932 (m-80) cc_final: 0.6396 (m-80) REVERT: A 266 TYR cc_start: 0.3435 (m-10) cc_final: 0.2520 (m-10) REVERT: A 378 LYS cc_start: 0.7438 (pttm) cc_final: 0.7182 (pttm) REVERT: A 398 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7420 (m-30) REVERT: A 434 ILE cc_start: 0.8340 (mp) cc_final: 0.8010 (mt) REVERT: A 451 TYR cc_start: 0.8272 (m-10) cc_final: 0.7947 (m-80) REVERT: A 455 LEU cc_start: 0.8288 (tp) cc_final: 0.8045 (tt) REVERT: A 516 GLU cc_start: 0.7168 (tt0) cc_final: 0.6784 (tt0) REVERT: A 529 LYS cc_start: 0.7785 (mmmm) cc_final: 0.7358 (mmmm) REVERT: A 556 ASN cc_start: 0.7745 (m-40) cc_final: 0.7492 (m-40) REVERT: A 565 PHE cc_start: 0.6424 (t80) cc_final: 0.6150 (t80) REVERT: A 587 ILE cc_start: 0.8787 (mt) cc_final: 0.8542 (mt) REVERT: A 612 TYR cc_start: 0.7429 (m-80) cc_final: 0.6316 (m-80) REVERT: A 627 ASP cc_start: 0.5285 (p0) cc_final: 0.4634 (p0) REVERT: A 629 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7090 (mt) REVERT: B 9 SER cc_start: 0.7828 (m) cc_final: 0.7579 (p) REVERT: B 42 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7890 (mttp) REVERT: B 54 LEU cc_start: 0.8207 (mp) cc_final: 0.7985 (mm) REVERT: B 97 THR cc_start: 0.8651 (t) cc_final: 0.8346 (p) REVERT: B 108 ARG cc_start: 0.7149 (mmt90) cc_final: 0.6832 (mmt90) REVERT: B 142 ARG cc_start: 0.7509 (ptp90) cc_final: 0.7035 (ptp90) REVERT: B 181 LEU cc_start: 0.8364 (mt) cc_final: 0.8064 (tp) REVERT: C 38 ARG cc_start: 0.8376 (ttp-170) cc_final: 0.8134 (mtp180) REVERT: C 75 LYS cc_start: 0.8534 (ptmt) cc_final: 0.8216 (ptpp) REVERT: C 133 LEU cc_start: 0.4645 (OUTLIER) cc_final: 0.4057 (pp) outliers start: 54 outliers final: 45 residues processed: 261 average time/residue: 0.2351 time to fit residues: 80.9644 Evaluate side-chains 281 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 231 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 206 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 0.0570 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8920 Z= 0.208 Angle : 0.668 19.678 12149 Z= 0.331 Chirality : 0.047 0.323 1355 Planarity : 0.005 0.062 1563 Dihedral : 6.016 53.657 1241 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.85 % Favored : 88.06 % Rotamer: Outliers : 5.52 % Allowed : 19.20 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.07 (0.23), residues: 1114 helix: -3.06 (0.81), residues: 30 sheet: -1.59 (0.29), residues: 300 loop : -2.33 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 34 HIS 0.003 0.001 HIS A 67 PHE 0.018 0.001 PHE B 118 TYR 0.022 0.001 TYR C 50 ARG 0.005 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 226 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.6919 (mm) REVERT: A 60 PHE cc_start: 0.6938 (m-80) cc_final: 0.6410 (m-80) REVERT: A 266 TYR cc_start: 0.3503 (m-10) cc_final: 0.2563 (m-10) REVERT: A 378 LYS cc_start: 0.7339 (pttm) cc_final: 0.7136 (pttm) REVERT: A 386 LYS cc_start: 0.7126 (mtmp) cc_final: 0.6889 (mtmp) REVERT: A 398 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7439 (m-30) REVERT: A 422 ASN cc_start: 0.7399 (m-40) cc_final: 0.7134 (m-40) REVERT: A 434 ILE cc_start: 0.8341 (mp) cc_final: 0.8040 (mt) REVERT: A 451 TYR cc_start: 0.8288 (m-10) cc_final: 0.7965 (m-80) REVERT: A 455 LEU cc_start: 0.8299 (tp) cc_final: 0.8051 (tt) REVERT: A 516 GLU cc_start: 0.7167 (tt0) cc_final: 0.6761 (tt0) REVERT: A 529 LYS cc_start: 0.7875 (mmmm) cc_final: 0.7449 (mmmm) REVERT: A 556 ASN cc_start: 0.7743 (m-40) cc_final: 0.7489 (m-40) REVERT: A 578 ASP cc_start: 0.7295 (m-30) cc_final: 0.6802 (m-30) REVERT: A 583 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7323 (mp0) REVERT: A 587 ILE cc_start: 0.8805 (mt) cc_final: 0.8548 (mt) REVERT: A 612 TYR cc_start: 0.7465 (m-80) cc_final: 0.6324 (m-80) REVERT: A 627 ASP cc_start: 0.5270 (p0) cc_final: 0.4670 (p0) REVERT: A 629 LEU cc_start: 0.7583 (mm) cc_final: 0.7086 (mt) REVERT: B 9 SER cc_start: 0.7821 (m) cc_final: 0.7558 (p) REVERT: B 42 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7895 (mttp) REVERT: B 97 THR cc_start: 0.8608 (t) cc_final: 0.8344 (p) REVERT: B 108 ARG cc_start: 0.7164 (mmt90) cc_final: 0.6855 (mmt90) REVERT: B 142 ARG cc_start: 0.7524 (ptp90) cc_final: 0.7045 (ptp90) REVERT: B 160 GLN cc_start: 0.7382 (mt0) cc_final: 0.7113 (mt0) REVERT: B 181 LEU cc_start: 0.8404 (mt) cc_final: 0.8101 (tp) REVERT: C 38 ARG cc_start: 0.8388 (ttp-170) cc_final: 0.8157 (mtp180) REVERT: C 75 LYS cc_start: 0.8561 (ptmt) cc_final: 0.8266 (ptpp) REVERT: C 179 LEU cc_start: 0.7793 (mt) cc_final: 0.7439 (tp) outliers start: 54 outliers final: 45 residues processed: 255 average time/residue: 0.2356 time to fit residues: 79.4045 Evaluate side-chains 274 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 226 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 206 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 0.0370 chunk 59 optimal weight: 0.0870 chunk 43 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.0270 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 63 optimal weight: 0.0980 overall best weight: 0.2494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8920 Z= 0.162 Angle : 0.654 19.636 12149 Z= 0.322 Chirality : 0.046 0.310 1355 Planarity : 0.004 0.061 1563 Dihedral : 5.858 52.460 1241 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.52 % Favored : 90.39 % Rotamer: Outliers : 4.39 % Allowed : 20.12 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.90 (0.23), residues: 1114 helix: -3.29 (0.82), residues: 30 sheet: -1.32 (0.30), residues: 277 loop : -2.25 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 148 HIS 0.003 0.001 HIS A 245 PHE 0.016 0.001 PHE B 118 TYR 0.023 0.001 TYR C 50 ARG 0.007 0.001 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 228 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7875 (mt) cc_final: 0.6875 (mm) REVERT: A 60 PHE cc_start: 0.6850 (m-80) cc_final: 0.6362 (m-80) REVERT: A 266 TYR cc_start: 0.3347 (m-10) cc_final: 0.2450 (m-10) REVERT: A 317 ASN cc_start: 0.6485 (t0) cc_final: 0.6112 (m-40) REVERT: A 355 ARG cc_start: 0.7338 (ttm170) cc_final: 0.6907 (ttt180) REVERT: A 364 ASP cc_start: 0.6887 (t70) cc_final: 0.6542 (t0) REVERT: A 386 LYS cc_start: 0.7149 (mtmp) cc_final: 0.6884 (mtmp) REVERT: A 434 ILE cc_start: 0.8209 (mp) cc_final: 0.7910 (mt) REVERT: A 451 TYR cc_start: 0.8257 (m-10) cc_final: 0.7926 (m-80) REVERT: A 455 LEU cc_start: 0.8271 (tp) cc_final: 0.8046 (tt) REVERT: A 509 ARG cc_start: 0.7021 (mtt180) cc_final: 0.6572 (mmt90) REVERT: A 516 GLU cc_start: 0.7112 (tt0) cc_final: 0.6744 (tt0) REVERT: A 529 LYS cc_start: 0.7722 (mmmm) cc_final: 0.7278 (mmmm) REVERT: A 556 ASN cc_start: 0.7673 (m-40) cc_final: 0.7430 (m-40) REVERT: A 587 ILE cc_start: 0.8782 (mt) cc_final: 0.8522 (mt) REVERT: A 612 TYR cc_start: 0.7391 (m-80) cc_final: 0.6299 (m-80) REVERT: A 627 ASP cc_start: 0.5193 (p0) cc_final: 0.4608 (p0) REVERT: A 629 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7015 (mt) REVERT: A 656 VAL cc_start: 0.7108 (t) cc_final: 0.6786 (p) REVERT: B 9 SER cc_start: 0.7776 (m) cc_final: 0.7477 (p) REVERT: B 42 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7815 (mttp) REVERT: B 97 THR cc_start: 0.8604 (t) cc_final: 0.8329 (p) REVERT: B 108 ARG cc_start: 0.7118 (mmt90) cc_final: 0.6789 (mmt90) REVERT: B 142 ARG cc_start: 0.7514 (ptp90) cc_final: 0.7056 (ptp90) REVERT: B 160 GLN cc_start: 0.7408 (mt0) cc_final: 0.7089 (mt0) REVERT: B 181 LEU cc_start: 0.8437 (mt) cc_final: 0.8148 (tp) REVERT: C 133 LEU cc_start: 0.4413 (OUTLIER) cc_final: 0.3868 (pp) outliers start: 43 outliers final: 37 residues processed: 253 average time/residue: 0.2420 time to fit residues: 80.1483 Evaluate side-chains 265 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 225 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 206 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 0.0870 chunk 26 optimal weight: 6.9990 overall best weight: 1.3160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8920 Z= 0.292 Angle : 0.729 20.900 12149 Z= 0.365 Chirality : 0.049 0.317 1355 Planarity : 0.005 0.062 1563 Dihedral : 6.005 52.185 1237 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.20 % Favored : 86.62 % Rotamer: Outliers : 4.70 % Allowed : 20.43 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.96 (0.24), residues: 1114 helix: -3.25 (0.69), residues: 36 sheet: -1.42 (0.30), residues: 297 loop : -2.27 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 34 HIS 0.006 0.001 HIS A 67 PHE 0.051 0.002 PHE A 565 TYR 0.020 0.002 TYR C 50 ARG 0.011 0.001 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 232 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.6235 (OUTLIER) cc_final: 0.5994 (m-30) REVERT: A 57 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.6647 (mm) REVERT: A 60 PHE cc_start: 0.6955 (m-80) cc_final: 0.6398 (m-80) REVERT: A 266 TYR cc_start: 0.3720 (m-10) cc_final: 0.2730 (m-10) REVERT: A 273 ARG cc_start: 0.6769 (mtt180) cc_final: 0.6569 (mtt180) REVERT: A 320 VAL cc_start: 0.7687 (m) cc_final: 0.6925 (p) REVERT: A 392 PHE cc_start: 0.7155 (m-80) cc_final: 0.6793 (m-80) REVERT: A 398 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7542 (m-30) REVERT: A 434 ILE cc_start: 0.8371 (mp) cc_final: 0.8088 (mt) REVERT: A 455 LEU cc_start: 0.8342 (tp) cc_final: 0.8069 (tt) REVERT: A 516 GLU cc_start: 0.7128 (tt0) cc_final: 0.6693 (tt0) REVERT: A 529 LYS cc_start: 0.8053 (mmmm) cc_final: 0.7596 (mmmm) REVERT: A 556 ASN cc_start: 0.7758 (m-40) cc_final: 0.7503 (m-40) REVERT: A 578 ASP cc_start: 0.7274 (m-30) cc_final: 0.6739 (m-30) REVERT: A 583 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7284 (mp0) REVERT: A 612 TYR cc_start: 0.7529 (m-80) cc_final: 0.6368 (m-80) REVERT: A 627 ASP cc_start: 0.5376 (p0) cc_final: 0.4935 (p0) REVERT: A 629 LEU cc_start: 0.7598 (mm) cc_final: 0.7125 (mt) REVERT: B 9 SER cc_start: 0.7834 (m) cc_final: 0.7569 (p) REVERT: B 42 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7995 (mttp) REVERT: B 97 THR cc_start: 0.8642 (t) cc_final: 0.8387 (p) REVERT: B 108 ARG cc_start: 0.7223 (mmt90) cc_final: 0.6885 (mmt90) REVERT: B 142 ARG cc_start: 0.7555 (ptp90) cc_final: 0.7090 (ptp90) REVERT: C 43 LYS cc_start: 0.8047 (mtmt) cc_final: 0.7820 (mtmt) REVERT: C 99 TYR cc_start: 0.8210 (t80) cc_final: 0.7989 (t80) REVERT: C 133 LEU cc_start: 0.4999 (OUTLIER) cc_final: 0.4363 (pp) REVERT: C 187 LEU cc_start: 0.7694 (pp) cc_final: 0.7324 (pt) REVERT: C 218 LYS cc_start: 0.7950 (mmmm) cc_final: 0.7643 (tppp) outliers start: 46 outliers final: 38 residues processed: 255 average time/residue: 0.2434 time to fit residues: 81.2842 Evaluate side-chains 271 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 228 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 206 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.191229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.158986 restraints weight = 15308.648| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 3.88 r_work: 0.3901 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8920 Z= 0.215 Angle : 0.704 19.117 12149 Z= 0.349 Chirality : 0.048 0.305 1355 Planarity : 0.005 0.061 1563 Dihedral : 5.965 52.207 1237 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.31 % Favored : 88.51 % Rotamer: Outliers : 4.09 % Allowed : 20.94 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.88 (0.24), residues: 1114 helix: -3.10 (0.76), residues: 30 sheet: -1.38 (0.30), residues: 298 loop : -2.22 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 34 HIS 0.004 0.001 HIS A 67 PHE 0.015 0.001 PHE B 118 TYR 0.024 0.001 TYR A 473 ARG 0.009 0.001 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2505.65 seconds wall clock time: 45 minutes 6.04 seconds (2706.04 seconds total)