Starting phenix.real_space_refine on Thu Jul 31 00:41:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vwi_21417/07_2025/6vwi_21417_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vwi_21417/07_2025/6vwi_21417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vwi_21417/07_2025/6vwi_21417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vwi_21417/07_2025/6vwi_21417.map" model { file = "/net/cci-nas-00/data/ceres_data/6vwi_21417/07_2025/6vwi_21417_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vwi_21417/07_2025/6vwi_21417_trim.cif" } resolution = 3.7 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= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 4078 2.51 5 N 1115 2.21 5 O 1224 1.98 5 H 6283 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12752 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6916 Classifications: {'peptide': 439} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 422} Chain breaks: 3 Chain: "B" Number of atoms: 4981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 4981 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 11, 'TRANS': 295} Chain breaks: 2 Chain: "I" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 799 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.85, per 1000 atoms: 0.54 Number of scatterers: 12752 At special positions: 0 Unit cell: (78.44, 110.24, 107.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1224 8.00 N 1115 7.00 C 4078 6.00 H 6283 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.02 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.02 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.02 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 458 " distance=2.03 Simple disulfide: pdb=" SG CYS I 9 " - pdb=" SG CYS I 47 " distance=2.02 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 60 " distance=2.03 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 51 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 21 " " NAG A1002 " - " ASN A 387 " " NAG A1003 " - " ASN A 105 " " NAG B1001 " - " ASN B 504 " Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 988.1 milliseconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1498 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 18 sheets defined 21.2% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.791A pdb=" N LYS A 17 " --> pdb=" O GLN A 14 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASN A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 43 removed outlier: 3.681A pdb=" N TYR A 43 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.798A pdb=" N CYS A 148 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 313 through 319 removed outlier: 3.661A pdb=" N MET A 319 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 removed outlier: 4.004A pdb=" N ASN A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'B' and resid 313 through 318 Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.908A pdb=" N GLU B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 removed outlier: 3.747A pdb=" N ILE B 429 " --> pdb=" O CYS B 425 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 447 Processing helix chain 'B' and resid 486 through 488 No H-bonds generated for 'chain 'B' and resid 486 through 488' Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 683 through 701 removed outlier: 5.028A pdb=" N ARG B 689 " --> pdb=" O GLU B 685 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N PHE B 692 " --> pdb=" O TYR B 688 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 701 " --> pdb=" O HIS B 697 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 22 Processing helix chain 'I' and resid 41 through 47 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 3.520A pdb=" N ILE A 76 " --> pdb=" O ASN A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 9 removed outlier: 6.819A pdb=" N ILE A 7 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N LEU A 32 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 29 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE A 58 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE A 31 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE A 90 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 57 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ARG A 112 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N GLU A 114 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE A 111 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 140 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE A 113 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 165 Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.561A pdb=" N THR A 177 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=AA6, first strand: chain 'A' and resid 205 through 209 removed outlier: 3.548A pdb=" N ALA A 220 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER A 208 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N CYS A 218 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA8, first strand: chain 'A' and resid 239 through 241 Processing sheet with id=AA9, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AB1, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AB2, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AB3, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.650A pdb=" N LEU A 331 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 358 through 361 removed outlier: 6.659A pdb=" N VAL A 358 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N LEU A 393 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 360 " --> pdb=" O LEU A 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 301 through 311 removed outlier: 5.991A pdb=" N ILE B 325 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLU B 303 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LYS B 327 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU B 305 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N ASN B 329 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS B 307 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU B 331 " --> pdb=" O LYS B 307 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS B 309 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 301 through 311 removed outlier: 5.991A pdb=" N ILE B 325 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLU B 303 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LYS B 327 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU B 305 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N ASN B 329 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS B 307 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU B 331 " --> pdb=" O LYS B 307 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS B 309 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N LYS B 359 " --> pdb=" O GLY B 328 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 330 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ARG B 361 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE B 332 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N TYR B 417 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR B 391 " --> pdb=" O TYR B 417 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ALA B 419 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU B 393 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 461 through 463 removed outlier: 5.894A pdb=" N ASP B 461 " --> pdb=" O LYS B 568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 465 through 470 removed outlier: 3.694A pdb=" N SER B 467 " --> pdb=" O THR B 478 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 520 through 524 removed outlier: 3.845A pdb=" N SER B 492 " --> pdb=" O VAL B 554 " (cutoff:3.500A) 136 hydrogen bonds defined for protein. 315 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: 4.36 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6282 1.03 - 1.23: 150 1.23 - 1.43: 2645 1.43 - 1.63: 3734 1.63 - 1.83: 67 Bond restraints: 12878 Sorted by residual: bond pdb=" C1 NAG A1002 " pdb=" O5 NAG A1002 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" C1 NAG A1003 " pdb=" C2 NAG A1003 " ideal model delta sigma weight residual 1.532 1.486 0.046 2.00e-02 2.50e+03 5.28e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.85e+00 bond pdb=" N SER I 5 " pdb=" CA SER I 5 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 bond pdb=" C1 NAG A1001 " pdb=" O5 NAG A1001 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 12873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 20886 1.21 - 2.42: 2053 2.42 - 3.64: 207 3.64 - 4.85: 33 4.85 - 6.06: 9 Bond angle restraints: 23188 Sorted by residual: angle pdb=" N LYS A 373 " pdb=" CA LYS A 373 " pdb=" C LYS A 373 " ideal model delta sigma weight residual 111.11 115.51 -4.40 1.20e+00 6.94e-01 1.35e+01 angle pdb=" N ARG B 407 " pdb=" CA ARG B 407 " pdb=" C ARG B 407 " ideal model delta sigma weight residual 108.69 114.45 -5.76 1.77e+00 3.19e-01 1.06e+01 angle pdb=" CA TRP B 544 " pdb=" CB TRP B 544 " pdb=" CG TRP B 544 " ideal model delta sigma weight residual 113.60 119.04 -5.44 1.90e+00 2.77e-01 8.19e+00 angle pdb=" N ASN A 11 " pdb=" CA ASN A 11 " pdb=" C ASN A 11 " ideal model delta sigma weight residual 110.80 116.86 -6.06 2.13e+00 2.20e-01 8.09e+00 angle pdb=" N LEU B 366 " pdb=" CA LEU B 366 " pdb=" C LEU B 366 " ideal model delta sigma weight residual 107.99 112.67 -4.68 1.77e+00 3.19e-01 6.99e+00 ... (remaining 23183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5496 17.65 - 35.30: 436 35.30 - 52.95: 124 52.95 - 70.60: 82 70.60 - 88.25: 12 Dihedral angle restraints: 6150 sinusoidal: 3404 harmonic: 2746 Sorted by residual: dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 181 " pdb=" CB CYS A 181 " ideal model delta sinusoidal sigma weight residual -86.00 -164.87 78.87 1 1.00e+01 1.00e-02 7.75e+01 dihedral pdb=" CA ASN B 374 " pdb=" C ASN B 374 " pdb=" N LEU B 375 " pdb=" CA LEU B 375 " ideal model delta harmonic sigma weight residual -180.00 -151.07 -28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CB CYS A 252 " pdb=" SG CYS A 252 " pdb=" SG CYS A 273 " pdb=" CB CYS A 273 " ideal model delta sinusoidal sigma weight residual -86.00 -135.20 49.20 1 1.00e+01 1.00e-02 3.33e+01 ... (remaining 6147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 525 0.035 - 0.069: 293 0.069 - 0.104: 126 0.104 - 0.138: 42 0.138 - 0.173: 5 Chirality restraints: 991 Sorted by residual: chirality pdb=" CA CYS I 46 " pdb=" N CYS I 46 " pdb=" C CYS I 46 " pdb=" CB CYS I 46 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" C2 NAG A1002 " pdb=" C1 NAG A1002 " pdb=" C3 NAG A1002 " pdb=" N2 NAG A1002 " both_signs ideal model delta sigma weight residual False -2.49 -2.34 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" C1 NAG A1003 " pdb=" ND2 ASN A 105 " pdb=" C2 NAG A1003 " pdb=" O5 NAG A1003 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 988 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 395 " 0.055 2.00e-02 2.50e+03 6.42e-02 6.19e+01 pdb=" CG ASN A 395 " -0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN A 395 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 395 " -0.094 2.00e-02 2.50e+03 pdb="HD21 ASN A 395 " -0.003 2.00e-02 2.50e+03 pdb="HD22 ASN A 395 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 336 " -0.150 9.50e-02 1.11e+02 6.80e-02 5.02e+01 pdb=" NE ARG A 336 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG A 336 " 0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG A 336 " -0.067 2.00e-02 2.50e+03 pdb=" NH2 ARG A 336 " 0.025 2.00e-02 2.50e+03 pdb="HH11 ARG A 336 " -0.027 2.00e-02 2.50e+03 pdb="HH12 ARG A 336 " 0.075 2.00e-02 2.50e+03 pdb="HH21 ARG A 336 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 336 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 395 " -0.041 2.00e-02 2.50e+03 5.08e-02 3.86e+01 pdb=" CG ASN B 395 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B 395 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 395 " 0.080 2.00e-02 2.50e+03 pdb="HD21 ASN B 395 " 0.001 2.00e-02 2.50e+03 pdb="HD22 ASN B 395 " -0.077 2.00e-02 2.50e+03 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 494 2.13 - 2.75: 23964 2.75 - 3.37: 34936 3.37 - 3.98: 44530 3.98 - 4.60: 70137 Nonbonded interactions: 174061 Sorted by model distance: nonbonded pdb=" HG1 THR A 195 " pdb=" O CYS A 209 " model vdw 1.513 2.450 nonbonded pdb="HH11 ARG A 174 " pdb=" OE1 GLN A 182 " model vdw 1.546 2.450 nonbonded pdb=" H CYS I 9 " pdb=" OE2 GLU I 12 " model vdw 1.548 2.450 nonbonded pdb=" O ALA A 61 " pdb="HD21 ASN A 94 " model vdw 1.572 2.450 nonbonded pdb=" HZ2 LYS A 164 " pdb=" OH TYR A 171 " model vdw 1.597 2.450 ... (remaining 174056 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.230 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: 0.220 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 29.400 Find NCS groups from input model: 0.100 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 : 0.007 0.053 6617 Z= 0.281 Angle : 0.883 6.059 8956 Z= 0.499 Chirality : 0.051 0.173 991 Planarity : 0.008 0.108 1140 Dihedral : 14.894 88.250 2524 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 1.97 % Allowed : 6.60 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.44 (0.28), residues: 782 helix: -3.51 (0.33), residues: 101 sheet: -0.76 (0.46), residues: 118 loop : -1.53 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.007 TRP A 176 HIS 0.009 0.003 HIS A 362 PHE 0.022 0.004 PHE A 45 TYR 0.040 0.007 TYR A 138 ARG 0.080 0.013 ARG A 104 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 4) link_NAG-ASN : angle 2.23797 ( 12) hydrogen bonds : bond 0.22043 ( 136) hydrogen bonds : angle 9.91789 ( 315) SS BOND : bond 0.00421 ( 18) SS BOND : angle 1.26709 ( 36) covalent geometry : bond 0.00679 ( 6595) covalent geometry : angle 0.87789 ( 8908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8325 (t80) cc_final: 0.8116 (t80) REVERT: A 256 LEU cc_start: 0.8342 (tp) cc_final: 0.7776 (pt) REVERT: A 266 PHE cc_start: 0.4675 (OUTLIER) cc_final: 0.4319 (t80) REVERT: A 333 ASN cc_start: 0.7847 (OUTLIER) cc_final: 0.7500 (t0) REVERT: B 396 GLN cc_start: 0.7956 (mt0) cc_final: 0.7691 (mt0) REVERT: B 572 LEU cc_start: 0.8623 (tp) cc_final: 0.8322 (tp) REVERT: I 44 GLU cc_start: 0.7835 (tt0) cc_final: 0.7278 (tt0) outliers start: 14 outliers final: 3 residues processed: 148 average time/residue: 0.4814 time to fit residues: 91.3140 Evaluate side-chains 80 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain I residue 8 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 197 ASN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN B 387 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.107073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.090253 restraints weight = 47167.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.094281 restraints weight = 21626.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.097023 restraints weight = 12740.789| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6617 Z= 0.151 Angle : 0.714 12.207 8956 Z= 0.384 Chirality : 0.047 0.159 991 Planarity : 0.005 0.079 1140 Dihedral : 8.876 56.500 970 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.11 % Allowed : 11.24 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.29), residues: 782 helix: -2.08 (0.46), residues: 108 sheet: -1.16 (0.46), residues: 110 loop : -1.19 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 402 HIS 0.004 0.001 HIS A 362 PHE 0.018 0.002 PHE A 326 TYR 0.011 0.001 TYR B 391 ARG 0.003 0.001 ARG B 481 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 4) link_NAG-ASN : angle 1.55943 ( 12) hydrogen bonds : bond 0.04605 ( 136) hydrogen bonds : angle 7.32589 ( 315) SS BOND : bond 0.00455 ( 18) SS BOND : angle 2.98006 ( 36) covalent geometry : bond 0.00343 ( 6595) covalent geometry : angle 0.68782 ( 8908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.8222 (t0) cc_final: 0.8018 (t0) REVERT: A 118 ASP cc_start: 0.7596 (t0) cc_final: 0.7249 (t70) REVERT: A 312 ASP cc_start: 0.6664 (t0) cc_final: 0.5995 (t0) REVERT: A 333 ASN cc_start: 0.7498 (t0) cc_final: 0.7241 (t0) REVERT: A 398 LEU cc_start: 0.8390 (tp) cc_final: 0.8173 (tt) REVERT: A 439 LYS cc_start: 0.7846 (mttt) cc_final: 0.6759 (tptt) REVERT: B 406 HIS cc_start: 0.6673 (OUTLIER) cc_final: 0.6415 (m-70) REVERT: B 420 PHE cc_start: 0.7670 (m-80) cc_final: 0.7447 (m-80) REVERT: I 44 GLU cc_start: 0.7951 (tt0) cc_final: 0.7423 (tt0) outliers start: 15 outliers final: 10 residues processed: 104 average time/residue: 0.3981 time to fit residues: 55.1702 Evaluate side-chains 83 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 674 LYS Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 65 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.116396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.100290 restraints weight = 46068.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.104388 restraints weight = 21186.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.107086 restraints weight = 12467.298| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6617 Z= 0.141 Angle : 0.625 7.292 8956 Z= 0.335 Chirality : 0.046 0.162 991 Planarity : 0.003 0.030 1140 Dihedral : 7.790 54.688 963 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 1.83 % Allowed : 12.92 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.29), residues: 782 helix: -1.53 (0.49), residues: 108 sheet: -1.34 (0.42), residues: 120 loop : -1.13 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 402 HIS 0.003 0.001 HIS A 362 PHE 0.012 0.001 PHE A 45 TYR 0.011 0.001 TYR B 391 ARG 0.003 0.000 ARG A 455 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 4) link_NAG-ASN : angle 1.26471 ( 12) hydrogen bonds : bond 0.04003 ( 136) hydrogen bonds : angle 6.52965 ( 315) SS BOND : bond 0.00391 ( 18) SS BOND : angle 2.05854 ( 36) covalent geometry : bond 0.00327 ( 6595) covalent geometry : angle 0.61069 ( 8908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.8237 (t0) cc_final: 0.7993 (t0) REVERT: A 266 PHE cc_start: 0.5217 (OUTLIER) cc_final: 0.4442 (t80) REVERT: A 439 LYS cc_start: 0.7634 (mttt) cc_final: 0.7245 (mmtt) outliers start: 13 outliers final: 7 residues processed: 88 average time/residue: 0.3650 time to fit residues: 43.8468 Evaluate side-chains 77 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 60 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.0570 chunk 44 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.113882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.098369 restraints weight = 45366.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.102349 restraints weight = 20779.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.104960 restraints weight = 12305.701| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6617 Z= 0.138 Angle : 0.612 6.722 8956 Z= 0.327 Chirality : 0.046 0.153 991 Planarity : 0.003 0.032 1140 Dihedral : 7.435 54.803 963 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.53 % Allowed : 12.92 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.30), residues: 782 helix: -1.48 (0.49), residues: 108 sheet: -1.52 (0.42), residues: 120 loop : -1.04 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 402 HIS 0.007 0.001 HIS A 202 PHE 0.011 0.001 PHE A 45 TYR 0.011 0.001 TYR B 391 ARG 0.003 0.000 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 4) link_NAG-ASN : angle 1.22506 ( 12) hydrogen bonds : bond 0.03590 ( 136) hydrogen bonds : angle 6.44164 ( 315) SS BOND : bond 0.00484 ( 18) SS BOND : angle 1.78001 ( 36) covalent geometry : bond 0.00315 ( 6595) covalent geometry : angle 0.60158 ( 8908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.8262 (t0) cc_final: 0.8029 (t0) REVERT: B 402 TRP cc_start: 0.6432 (OUTLIER) cc_final: 0.5784 (p-90) outliers start: 18 outliers final: 11 residues processed: 84 average time/residue: 0.4257 time to fit residues: 47.2369 Evaluate side-chains 76 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 60 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.112773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.097187 restraints weight = 45285.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.101159 restraints weight = 20987.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.103731 restraints weight = 12476.237| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6617 Z= 0.153 Angle : 0.587 6.661 8956 Z= 0.314 Chirality : 0.045 0.154 991 Planarity : 0.003 0.038 1140 Dihedral : 7.251 54.607 963 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.95 % Allowed : 14.47 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.30), residues: 782 helix: -1.45 (0.48), residues: 108 sheet: -1.63 (0.44), residues: 108 loop : -1.14 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 402 HIS 0.002 0.001 HIS A 362 PHE 0.012 0.001 PHE A 45 TYR 0.014 0.001 TYR B 550 ARG 0.003 0.000 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 4) link_NAG-ASN : angle 1.21529 ( 12) hydrogen bonds : bond 0.03536 ( 136) hydrogen bonds : angle 6.36453 ( 315) SS BOND : bond 0.00364 ( 18) SS BOND : angle 1.22932 ( 36) covalent geometry : bond 0.00345 ( 6595) covalent geometry : angle 0.58204 ( 8908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 402 TRP cc_start: 0.6552 (OUTLIER) cc_final: 0.5797 (p-90) outliers start: 21 outliers final: 13 residues processed: 79 average time/residue: 0.3405 time to fit residues: 37.9395 Evaluate side-chains 72 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 60 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 65 optimal weight: 0.0980 chunk 42 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.113666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.098113 restraints weight = 45448.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.102108 restraints weight = 20830.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.104704 restraints weight = 12290.331| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6617 Z= 0.112 Angle : 0.548 6.367 8956 Z= 0.291 Chirality : 0.044 0.154 991 Planarity : 0.003 0.041 1140 Dihedral : 6.804 53.945 963 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.53 % Allowed : 14.75 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.30), residues: 782 helix: -1.22 (0.50), residues: 107 sheet: -1.70 (0.45), residues: 109 loop : -1.16 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 402 HIS 0.004 0.001 HIS B 364 PHE 0.008 0.001 PHE B 493 TYR 0.012 0.001 TYR B 550 ARG 0.002 0.000 ARG B 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 4) link_NAG-ASN : angle 1.07403 ( 12) hydrogen bonds : bond 0.03161 ( 136) hydrogen bonds : angle 6.07729 ( 315) SS BOND : bond 0.00227 ( 18) SS BOND : angle 0.95442 ( 36) covalent geometry : bond 0.00254 ( 6595) covalent geometry : angle 0.54436 ( 8908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 266 PHE cc_start: 0.5103 (OUTLIER) cc_final: 0.4110 (t80) REVERT: B 311 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.7946 (mp) REVERT: B 402 TRP cc_start: 0.6535 (OUTLIER) cc_final: 0.5678 (p-90) outliers start: 18 outliers final: 11 residues processed: 79 average time/residue: 0.3569 time to fit residues: 39.3381 Evaluate side-chains 76 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 60 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 0.0020 chunk 43 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.113234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.097523 restraints weight = 45161.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.101503 restraints weight = 21045.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.104071 restraints weight = 12585.281| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6617 Z= 0.127 Angle : 0.552 6.153 8956 Z= 0.294 Chirality : 0.044 0.146 991 Planarity : 0.003 0.043 1140 Dihedral : 6.733 53.572 963 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.80 % Favored : 92.07 % Rotamer: Outliers : 2.39 % Allowed : 14.33 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.29), residues: 782 helix: -1.27 (0.48), residues: 107 sheet: -1.66 (0.45), residues: 108 loop : -1.21 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 402 HIS 0.002 0.000 HIS A 362 PHE 0.010 0.001 PHE A 45 TYR 0.012 0.001 TYR B 550 ARG 0.002 0.000 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 4) link_NAG-ASN : angle 1.09896 ( 12) hydrogen bonds : bond 0.03195 ( 136) hydrogen bonds : angle 6.03819 ( 315) SS BOND : bond 0.00257 ( 18) SS BOND : angle 1.06408 ( 36) covalent geometry : bond 0.00285 ( 6595) covalent geometry : angle 0.54784 ( 8908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.7940 (mp) REVERT: B 402 TRP cc_start: 0.6646 (OUTLIER) cc_final: 0.5736 (p-90) outliers start: 17 outliers final: 12 residues processed: 76 average time/residue: 0.3855 time to fit residues: 39.8998 Evaluate side-chains 74 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 60 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 0.0170 chunk 77 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.114724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.099050 restraints weight = 45228.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.103115 restraints weight = 20713.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.105746 restraints weight = 12250.802| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6617 Z= 0.099 Angle : 0.533 5.993 8956 Z= 0.282 Chirality : 0.044 0.145 991 Planarity : 0.003 0.040 1140 Dihedral : 6.363 54.343 963 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.65 % Favored : 93.22 % Rotamer: Outliers : 1.97 % Allowed : 15.17 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.29), residues: 782 helix: -1.15 (0.49), residues: 107 sheet: -1.64 (0.45), residues: 108 loop : -1.16 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 544 HIS 0.002 0.000 HIS A 362 PHE 0.009 0.001 PHE I 19 TYR 0.011 0.001 TYR B 550 ARG 0.003 0.000 ARG B 431 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 4) link_NAG-ASN : angle 0.98635 ( 12) hydrogen bonds : bond 0.02980 ( 136) hydrogen bonds : angle 5.82971 ( 315) SS BOND : bond 0.00224 ( 18) SS BOND : angle 0.96821 ( 36) covalent geometry : bond 0.00231 ( 6595) covalent geometry : angle 0.52962 ( 8908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 266 PHE cc_start: 0.4968 (OUTLIER) cc_final: 0.3974 (t80) REVERT: A 394 ASP cc_start: 0.7243 (t0) cc_final: 0.6961 (t0) REVERT: B 402 TRP cc_start: 0.6551 (OUTLIER) cc_final: 0.5723 (p-90) REVERT: B 432 MET cc_start: 0.7750 (tmm) cc_final: 0.7476 (tmm) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.3814 time to fit residues: 40.2929 Evaluate side-chains 73 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 60 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.103985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.087680 restraints weight = 47027.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.091565 restraints weight = 21291.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.094156 restraints weight = 12434.862| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6617 Z= 0.139 Angle : 0.556 6.313 8956 Z= 0.294 Chirality : 0.044 0.144 991 Planarity : 0.003 0.043 1140 Dihedral : 6.528 53.563 963 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.06 % Favored : 91.82 % Rotamer: Outliers : 2.11 % Allowed : 15.31 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.29), residues: 782 helix: -1.19 (0.48), residues: 107 sheet: -1.62 (0.47), residues: 103 loop : -1.25 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 402 HIS 0.002 0.000 HIS A 362 PHE 0.012 0.001 PHE A 45 TYR 0.013 0.001 TYR B 550 ARG 0.001 0.000 ARG A 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 4) link_NAG-ASN : angle 1.07021 ( 12) hydrogen bonds : bond 0.03069 ( 136) hydrogen bonds : angle 5.88668 ( 315) SS BOND : bond 0.00240 ( 18) SS BOND : angle 0.98176 ( 36) covalent geometry : bond 0.00314 ( 6595) covalent geometry : angle 0.55296 ( 8908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.7876 (mp) REVERT: B 402 TRP cc_start: 0.6690 (OUTLIER) cc_final: 0.5644 (p-90) outliers start: 15 outliers final: 12 residues processed: 71 average time/residue: 0.4051 time to fit residues: 39.0287 Evaluate side-chains 72 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 60 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.104111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.087864 restraints weight = 46937.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.091727 restraints weight = 21185.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.094299 restraints weight = 12351.163| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6617 Z= 0.124 Angle : 0.549 5.804 8956 Z= 0.289 Chirality : 0.044 0.147 991 Planarity : 0.003 0.042 1140 Dihedral : 6.433 54.022 963 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.16 % Favored : 92.71 % Rotamer: Outliers : 1.97 % Allowed : 15.31 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.29), residues: 782 helix: -1.12 (0.49), residues: 107 sheet: -1.64 (0.47), residues: 103 loop : -1.25 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 544 HIS 0.002 0.000 HIS A 362 PHE 0.009 0.001 PHE A 45 TYR 0.012 0.001 TYR B 550 ARG 0.002 0.000 ARG B 407 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 4) link_NAG-ASN : angle 1.02418 ( 12) hydrogen bonds : bond 0.02989 ( 136) hydrogen bonds : angle 5.82187 ( 315) SS BOND : bond 0.00221 ( 18) SS BOND : angle 0.98341 ( 36) covalent geometry : bond 0.00285 ( 6595) covalent geometry : angle 0.54554 ( 8908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 402 TRP cc_start: 0.6719 (OUTLIER) cc_final: 0.5662 (p-90) outliers start: 14 outliers final: 12 residues processed: 71 average time/residue: 0.3873 time to fit residues: 37.3472 Evaluate side-chains 72 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 60 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.0070 chunk 55 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.105471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.088963 restraints weight = 47473.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.092827 restraints weight = 21908.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.095426 restraints weight = 12978.347| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6617 Z= 0.103 Angle : 0.532 5.836 8956 Z= 0.280 Chirality : 0.044 0.143 991 Planarity : 0.003 0.039 1140 Dihedral : 6.216 54.085 963 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.03 % Favored : 92.84 % Rotamer: Outliers : 1.83 % Allowed : 15.31 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.29), residues: 782 helix: -1.04 (0.50), residues: 107 sheet: -1.59 (0.48), residues: 103 loop : -1.25 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 544 HIS 0.001 0.000 HIS A 362 PHE 0.009 0.001 PHE I 19 TYR 0.011 0.001 TYR B 550 ARG 0.002 0.000 ARG B 431 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 4) link_NAG-ASN : angle 0.98890 ( 12) hydrogen bonds : bond 0.02910 ( 136) hydrogen bonds : angle 5.73140 ( 315) SS BOND : bond 0.00200 ( 18) SS BOND : angle 0.98365 ( 36) covalent geometry : bond 0.00238 ( 6595) covalent geometry : angle 0.52827 ( 8908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4761.95 seconds wall clock time: 82 minutes 12.28 seconds (4932.28 seconds total)