Starting phenix.real_space_refine on Sat Jul 4 05:39:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p95_71399/07_2026/9p95_71399_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p95_71399/07_2026/9p95_71399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p95_71399/07_2026/9p95_71399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p95_71399/07_2026/9p95_71399.map" model { file = "/net/cci-nas-00/data/ceres_data/9p95_71399/07_2026/9p95_71399_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p95_71399/07_2026/9p95_71399_trim.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 Mn 3 7.51 5 S 42 5.16 5 C 5725 2.51 5 N 1576 2.21 5 O 1798 1.98 5 H 8719 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17866 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 8858 Classifications: {'peptide': 582} Link IDs: {'PTRANS': 26, 'TRANS': 555} 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: "B" Number of atoms: 5819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 5819 Classifications: {'peptide': 379} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 357} Chain: "C" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 2974 Classifications: {'peptide': 201} Link IDs: {'PCIS': 4, 'PTRANS': 14, 'TRANS': 182} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 14 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 14 Ad-hoc single atom residues: {' MN': 3} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" 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: 2.63, per 1000 atoms: 0.15 Number of scatterers: 17866 At special positions: 0 Unit cell: (81.906, 124.542, 153.714, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 3 24.99 Ca 3 19.99 S 42 16.00 O 1798 8.00 N 1576 7.00 C 5725 6.00 H 8719 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 85 " distance=2.03 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 132 " distance=2.03 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 165 " distance=2.02 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 409 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 29 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 112 " - pdb=" SG CYS C 182 " 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 ALPHA1-3 " BMA D 3 " - " MAN D 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A1001 " - " ASN A 447 " " NAG B 804 " - " ASN B 260 " " NAG C 401 " - " ASN C 61 " " NAG E 1 " - " ASN A 196 " " NAG F 1 " - " ASN A 46 " " NAG G 1 " - " ASN A 485 " Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 438.8 milliseconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 23 sheets defined 11.9% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'B' and resid 142 through 147 removed outlier: 4.489A pdb=" N ASP B 147 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 165 Processing helix chain 'B' and resid 189 through 195 Processing helix chain 'B' and resid 219 through 229 Processing helix chain 'B' and resid 241 through 252 removed outlier: 4.049A pdb=" N ALA B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.937A pdb=" N GLY B 257 " --> pdb=" O GLN B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 283 removed outlier: 4.075A pdb=" N GLY B 282 " --> pdb=" O ASP B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 306 removed outlier: 4.151A pdb=" N THR B 304 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 Processing helix chain 'B' and resid 333 through 344 removed outlier: 3.601A pdb=" N TYR B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS B 342 " --> pdb=" O GLN B 338 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 368 Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'C' and resid 63 through 67 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.636A pdb=" N SER A 424 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE A 405 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA A 416 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLY A 403 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLY A 418 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE A 401 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 28 removed outlier: 4.269A pdb=" N ILE A 55 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.570A pdb=" N LEU A 127 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 94 through 100 removed outlier: 3.870A pdb=" N THR A 97 " --> pdb=" O CYS A 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA6, first strand: chain 'A' and resid 222 through 225 removed outlier: 6.595A pdb=" N ALA A 248 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU A 263 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE A 250 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 277 through 278 Processing sheet with id=AA8, first strand: chain 'A' and resid 339 through 343 removed outlier: 5.998A pdb=" N ASP A 352 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 339 through 343 removed outlier: 5.998A pdb=" N ASP A 352 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 383 " --> pdb=" O ILE A 369 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 433 through 434 removed outlier: 6.174A pdb=" N ILE A 569 " --> pdb=" O VAL A 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 439 through 440 Processing sheet with id=AB3, first strand: chain 'A' and resid 453 through 455 removed outlier: 3.577A pdb=" N CYS A 453 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 513 through 518 Processing sheet with id=AB5, first strand: chain 'A' and resid 542 through 546 removed outlier: 3.519A pdb=" N ALA A 546 " --> pdb=" O MET A 579 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A 579 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 83 through 89 removed outlier: 4.129A pdb=" N GLN B 83 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG B 108 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP B 89 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLN B 107 " --> pdb=" O GLU B 446 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 119 through 126 removed outlier: 4.379A pdb=" N THR B 419 " --> pdb=" O GLN B 392 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER B 391 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 397 " --> pdb=" O CYS B 393 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 211 through 217 removed outlier: 7.042A pdb=" N VAL B 213 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N SER B 176 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N SER B 215 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N PHE B 174 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B 177 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG B 263 " --> pdb=" O GLN B 324 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ILE B 326 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU B 265 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ALA B 328 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE B 267 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 372 through 374 removed outlier: 6.533A pdb=" N VAL B 374 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASN B 410 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'C' and resid 12 through 16 removed outlier: 3.744A pdb=" N GLY C 68 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 35 through 39 removed outlier: 3.559A pdb=" N SER C 35 " --> pdb=" O SER C 75 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL C 71 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.842A pdb=" N ARG C 166 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY C 143 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG C 168 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA C 141 " --> pdb=" O ARG C 168 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 134 through 135 302 hydrogen bonds defined for protein. 774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 1.92 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: 8707 1.03 - 1.23: 139 1.23 - 1.43: 3827 1.43 - 1.62: 5326 1.62 - 1.82: 56 Bond restraints: 18055 Sorted by residual: bond pdb=" N SER A 559 " pdb=" H SER A 559 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C1 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sigma weight residual 1.410 1.472 -0.062 2.00e-02 2.50e+03 9.74e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.577 -0.058 2.00e-02 2.50e+03 8.42e+00 bond pdb=" CA ASN A 51 " pdb=" C ASN A 51 " ideal model delta sigma weight residual 1.534 1.516 0.018 9.50e-03 1.11e+04 3.52e+00 bond pdb=" C ARG C 168 " pdb=" N LEU C 169 " ideal model delta sigma weight residual 1.331 1.286 0.045 2.83e-02 1.25e+03 2.54e+00 ... (remaining 18050 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.20: 32492 7.20 - 14.41: 1 14.41 - 21.61: 0 21.61 - 28.82: 0 28.82 - 36.02: 6 Bond angle restraints: 32499 Sorted by residual: angle pdb=" C VAL A 413 " pdb=" CA VAL A 413 " pdb=" HA VAL A 413 " ideal model delta sigma weight residual 109.00 72.98 36.02 3.00e+00 1.11e-01 1.44e+02 angle pdb=" N VAL A 413 " pdb=" CA VAL A 413 " pdb=" HA VAL A 413 " ideal model delta sigma weight residual 110.00 74.09 35.91 3.00e+00 1.11e-01 1.43e+02 angle pdb=" C LEU A 488 " pdb=" CA LEU A 488 " pdb=" HA LEU A 488 " ideal model delta sigma weight residual 109.00 73.52 35.48 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N LEU A 488 " pdb=" CA LEU A 488 " pdb=" HA LEU A 488 " ideal model delta sigma weight residual 110.00 75.36 34.64 3.00e+00 1.11e-01 1.33e+02 angle pdb=" CB LEU A 488 " pdb=" CA LEU A 488 " pdb=" HA LEU A 488 " ideal model delta sigma weight residual 109.00 74.96 34.04 3.00e+00 1.11e-01 1.29e+02 ... (remaining 32494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7827 17.96 - 35.92: 659 35.92 - 53.88: 249 53.88 - 71.84: 68 71.84 - 89.80: 17 Dihedral angle restraints: 8820 sinusoidal: 4979 harmonic: 3841 Sorted by residual: dihedral pdb=" CB CYS B 393 " pdb=" SG CYS B 393 " pdb=" SG CYS B 409 " pdb=" CB CYS B 409 " ideal model delta sinusoidal sigma weight residual 93.00 148.54 -55.54 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CA GLY A 159 " pdb=" C GLY A 159 " pdb=" N GLU A 160 " pdb=" CA GLU A 160 " ideal model delta harmonic sigma weight residual -180.00 -152.64 -27.36 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ALA A 419 " pdb=" C ALA A 419 " pdb=" N PHE A 420 " pdb=" CA PHE A 420 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 8817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1199 0.066 - 0.132: 235 0.132 - 0.197: 15 0.197 - 0.263: 0 0.263 - 0.329: 3 Chirality restraints: 1452 Sorted by residual: chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.73e+00 chirality pdb=" CA VAL A 413 " pdb=" N VAL A 413 " pdb=" C VAL A 413 " pdb=" CB VAL A 413 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA LEU A 488 " pdb=" N LEU A 488 " pdb=" C LEU A 488 " pdb=" CB LEU A 488 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 1449 not shown) Planarity restraints: 2753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 7 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO C 8 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 8 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 8 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 166 " -0.161 9.50e-02 1.11e+02 5.44e-02 4.21e+00 pdb=" NE ARG C 166 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 166 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 166 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 166 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 166 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG C 166 " 0.004 2.00e-02 2.50e+03 pdb="HH21 ARG C 166 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG C 166 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 324 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO B 325 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 325 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 325 " -0.026 5.00e-02 4.00e+02 ... (remaining 2750 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1279 2.21 - 2.80: 37344 2.80 - 3.40: 47015 3.40 - 4.00: 64381 4.00 - 4.60: 98506 Nonbonded interactions: 248525 Sorted by model distance: nonbonded pdb=" HG SER B 144 " pdb="MN MN B 803 " model vdw 1.608 2.590 nonbonded pdb=" H LEU A 488 " pdb=" HA LEU A 488 " model vdw 1.671 1.816 nonbonded pdb=" H VAL A 413 " pdb=" HA VAL A 413 " model vdw 1.692 1.816 nonbonded pdb=" HA LEU A 488 " pdb=" HB2 LEU A 488 " model vdw 1.721 1.952 nonbonded pdb=" H SER B 144 " pdb=" HG SER B 144 " model vdw 1.815 2.100 ... (remaining 248520 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.390 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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 0.067 9359 Z= 0.318 Angle : 0.803 12.158 12740 Z= 0.433 Chirality : 0.050 0.329 1452 Planarity : 0.006 0.073 1654 Dihedral : 14.987 89.796 3676 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.61 % Allowed : 12.27 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.24), residues: 1154 helix: -1.57 (0.45), residues: 98 sheet: -1.10 (0.26), residues: 388 loop : -1.20 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 166 TYR 0.022 0.002 TYR A 120 PHE 0.029 0.003 PHE A 397 TRP 0.013 0.002 TRP A 93 HIS 0.007 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00707 / 0.32 ( 9336) covalent geometry : angle 0.76889 / 0.43 (12679) SS BOND : bond 0.00343 / 0.17 ( 8) SS BOND : angle 1.05884 / 0.61 ( 16) hydrogen bonds : bond 0.19851 / 13.82 ( 295) hydrogen bonds : angle 10.50687 / 7.25 ( 774) link_ALPHA1-3 : bond 0.01444 / 0.76 ( 1) link_ALPHA1-3 : angle 1.22774 / 0.71 ( 3) link_BETA1-4 : bond 0.02640 / 1.28 ( 8) link_BETA1-4 : angle 4.79445 / 3.12 ( 24) link_NAG-ASN : bond 0.00860 / 0.43 ( 6) link_NAG-ASN : angle 2.90569 / 1.72 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 179 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8095 (m) cc_final: 0.7811 (p) REVERT: A 122 LYS cc_start: 0.8122 (ttpt) cc_final: 0.7900 (ttpt) REVERT: A 227 PHE cc_start: 0.8346 (m-80) cc_final: 0.8145 (m-80) REVERT: A 299 THR cc_start: 0.8177 (m) cc_final: 0.7943 (p) REVERT: B 244 ASP cc_start: 0.7824 (m-30) cc_final: 0.7559 (m-30) outliers start: 6 outliers final: 4 residues processed: 183 average time/residue: 0.2484 time to fit residues: 59.0291 Evaluate side-chains 180 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 176 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain B residue 178 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.191214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140489 restraints weight = 35430.794| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.34 r_work: 0.3523 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 9359 Z= 0.352 Angle : 0.742 8.268 12740 Z= 0.387 Chirality : 0.052 0.334 1452 Planarity : 0.006 0.057 1654 Dihedral : 8.122 53.730 1588 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.23 % Allowed : 12.88 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.23), residues: 1154 helix: -1.56 (0.42), residues: 99 sheet: -0.89 (0.26), residues: 387 loop : -1.43 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 334 TYR 0.021 0.002 TYR A 220 PHE 0.029 0.003 PHE A 397 TRP 0.011 0.002 TRP A 93 HIS 0.008 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00807 / 0.35 ( 9336) covalent geometry : angle 0.71929 / 0.38 (12679) SS BOND : bond 0.00366 / 0.18 ( 8) SS BOND : angle 0.95195 / 0.52 ( 16) hydrogen bonds : bond 0.04931 / 3.35 ( 295) hydrogen bonds : angle 7.94185 / 5.46 ( 774) link_ALPHA1-3 : bond 0.01185 / 0.62 ( 1) link_ALPHA1-3 : angle 1.62921 / 0.93 ( 3) link_BETA1-4 : bond 0.00878 / 0.44 ( 8) link_BETA1-4 : angle 3.48807 / 2.27 ( 24) link_NAG-ASN : bond 0.00773 / 0.39 ( 6) link_NAG-ASN : angle 2.74958 / 1.64 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.315 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 48 SER cc_start: 0.8101 (m) cc_final: 0.7760 (p) REVERT: A 122 LYS cc_start: 0.8099 (ttpt) cc_final: 0.7833 (ttpt) REVERT: A 388 LEU cc_start: 0.7823 (tp) cc_final: 0.7590 (mp) REVERT: A 472 LYS cc_start: 0.8180 (ptpt) cc_final: 0.7925 (pttm) REVERT: A 525 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6333 (mmp80) REVERT: B 179 ASP cc_start: 0.6792 (p0) cc_final: 0.6497 (p0) outliers start: 12 outliers final: 10 residues processed: 191 average time/residue: 0.2380 time to fit residues: 58.8966 Evaluate side-chains 189 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 126 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 19 optimal weight: 0.2980 chunk 46 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 chunk 70 optimal weight: 0.2980 chunk 37 optimal weight: 0.4980 chunk 49 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 80 optimal weight: 0.0980 chunk 58 optimal weight: 50.0000 chunk 57 optimal weight: 8.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** B 235 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 = 0.4336 r_free = 0.4336 target = 0.193472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143200 restraints weight = 35610.430| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.41 r_work: 0.3550 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9359 Z= 0.150 Angle : 0.611 7.358 12740 Z= 0.318 Chirality : 0.046 0.342 1452 Planarity : 0.005 0.054 1654 Dihedral : 7.024 53.102 1585 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.43 % Allowed : 13.39 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.24), residues: 1154 helix: -0.78 (0.47), residues: 98 sheet: -0.80 (0.25), residues: 396 loop : -1.21 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 100 TYR 0.016 0.001 TYR A 21 PHE 0.016 0.001 PHE A 397 TRP 0.009 0.001 TRP A 115 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 9336) covalent geometry : angle 0.59422 / 0.31 (12679) SS BOND : bond 0.00223 / 0.11 ( 8) SS BOND : angle 0.73104 / 0.39 ( 16) hydrogen bonds : bond 0.03779 / 2.57 ( 295) hydrogen bonds : angle 7.14543 / 4.92 ( 774) link_ALPHA1-3 : bond 0.00785 / 0.41 ( 1) link_ALPHA1-3 : angle 1.39270 / 0.80 ( 3) link_BETA1-4 : bond 0.00741 / 0.37 ( 8) link_BETA1-4 : angle 2.76723 / 1.82 ( 24) link_NAG-ASN : bond 0.00305 / 0.16 ( 6) link_NAG-ASN : angle 2.08824 / 1.24 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8102 (m) cc_final: 0.7777 (p) REVERT: A 525 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.6238 (mmp80) REVERT: A 531 MET cc_start: 0.5957 (OUTLIER) cc_final: 0.5625 (pmm) REVERT: B 154 GLN cc_start: 0.7982 (mt0) cc_final: 0.7725 (mp10) REVERT: B 179 ASP cc_start: 0.6601 (p0) cc_final: 0.6366 (p0) outliers start: 14 outliers final: 9 residues processed: 193 average time/residue: 0.2230 time to fit residues: 56.4181 Evaluate side-chains 194 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 80 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 95 optimal weight: 0.0370 chunk 85 optimal weight: 0.9980 chunk 83 optimal weight: 0.0980 chunk 74 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 78 optimal weight: 0.0370 chunk 108 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 67 optimal weight: 0.0980 overall best weight: 0.1736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.195195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144890 restraints weight = 35379.360| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.41 r_work: 0.3583 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9359 Z= 0.111 Angle : 0.562 6.791 12740 Z= 0.291 Chirality : 0.046 0.342 1452 Planarity : 0.004 0.053 1654 Dihedral : 6.412 51.194 1585 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.23 % Allowed : 13.80 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.24), residues: 1154 helix: -0.21 (0.50), residues: 98 sheet: -0.65 (0.25), residues: 393 loop : -1.06 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 302 TYR 0.010 0.001 TYR A 331 PHE 0.011 0.001 PHE A 251 TRP 0.010 0.001 TRP A 115 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 9336) covalent geometry : angle 0.54792 / 0.29 (12679) SS BOND : bond 0.00277 / 0.14 ( 8) SS BOND : angle 0.63900 / 0.34 ( 16) hydrogen bonds : bond 0.02958 / 2.01 ( 295) hydrogen bonds : angle 6.52442 / 4.50 ( 774) link_ALPHA1-3 : bond 0.00677 / 0.36 ( 1) link_ALPHA1-3 : angle 1.47979 / 0.85 ( 3) link_BETA1-4 : bond 0.00651 / 0.33 ( 8) link_BETA1-4 : angle 2.37967 / 1.56 ( 24) link_NAG-ASN : bond 0.00275 / 0.15 ( 6) link_NAG-ASN : angle 1.85017 / 1.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8091 (m) cc_final: 0.7774 (p) REVERT: A 525 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.6229 (mmp80) REVERT: A 531 MET cc_start: 0.6027 (ptp) cc_final: 0.5744 (pmm) REVERT: B 154 GLN cc_start: 0.7985 (mt0) cc_final: 0.7730 (mp10) outliers start: 12 outliers final: 10 residues processed: 190 average time/residue: 0.2242 time to fit residues: 56.3822 Evaluate side-chains 193 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain C residue 80 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 86 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN ** A 242 HIS ** 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 = 0.4325 r_free = 0.4325 target = 0.192357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.141596 restraints weight = 35397.993| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.38 r_work: 0.3539 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9359 Z= 0.220 Angle : 0.607 6.706 12740 Z= 0.317 Chirality : 0.047 0.342 1452 Planarity : 0.005 0.053 1654 Dihedral : 6.504 52.501 1585 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.53 % Allowed : 13.80 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.24), residues: 1154 helix: -0.59 (0.47), residues: 104 sheet: -0.61 (0.26), residues: 391 loop : -1.21 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 100 TYR 0.014 0.002 TYR A 220 PHE 0.022 0.002 PHE A 397 TRP 0.013 0.002 TRP A 115 HIS 0.006 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 ( 9336) covalent geometry : angle 0.59365 / 0.31 (12679) SS BOND : bond 0.00273 / 0.14 ( 8) SS BOND : angle 0.77961 / 0.43 ( 16) hydrogen bonds : bond 0.03401 / 2.30 ( 295) hydrogen bonds : angle 6.53829 / 4.49 ( 774) link_ALPHA1-3 : bond 0.00668 / 0.35 ( 1) link_ALPHA1-3 : angle 1.47832 / 0.85 ( 3) link_BETA1-4 : bond 0.00563 / 0.28 ( 8) link_BETA1-4 : angle 2.33501 / 1.51 ( 24) link_NAG-ASN : bond 0.00470 / 0.25 ( 6) link_NAG-ASN : angle 1.99233 / 1.20 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.455 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 48 SER cc_start: 0.8099 (m) cc_final: 0.7765 (p) REVERT: A 90 ASP cc_start: 0.7538 (p0) cc_final: 0.7323 (p0) REVERT: A 525 ARG cc_start: 0.6439 (OUTLIER) cc_final: 0.6181 (mmp80) REVERT: A 531 MET cc_start: 0.6055 (ptp) cc_final: 0.5736 (pmm) REVERT: B 150 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6473 (mm-30) REVERT: B 154 GLN cc_start: 0.7979 (mt0) cc_final: 0.7419 (mp10) outliers start: 15 outliers final: 12 residues processed: 187 average time/residue: 0.2435 time to fit residues: 59.2989 Evaluate side-chains 191 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 80 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 73 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 HIS ** 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 = 0.4321 r_free = 0.4321 target = 0.192291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142173 restraints weight = 35164.021| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.34 r_work: 0.3543 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9359 Z= 0.229 Angle : 0.608 7.170 12740 Z= 0.319 Chirality : 0.047 0.342 1452 Planarity : 0.005 0.052 1654 Dihedral : 6.530 53.182 1585 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.45 % Allowed : 13.39 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.24), residues: 1154 helix: -0.78 (0.46), residues: 104 sheet: -0.68 (0.25), residues: 406 loop : -1.24 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 89 TYR 0.014 0.002 TYR A 220 PHE 0.023 0.002 PHE A 397 TRP 0.009 0.002 TRP C 167 HIS 0.006 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 ( 9336) covalent geometry : angle 0.59653 / 0.32 (12679) SS BOND : bond 0.00292 / 0.15 ( 8) SS BOND : angle 0.77577 / 0.43 ( 16) hydrogen bonds : bond 0.03377 / 2.27 ( 295) hydrogen bonds : angle 6.49007 / 4.45 ( 774) link_ALPHA1-3 : bond 0.00562 / 0.30 ( 1) link_ALPHA1-3 : angle 1.44320 / 0.83 ( 3) link_BETA1-4 : bond 0.00549 / 0.27 ( 8) link_BETA1-4 : angle 2.21032 / 1.41 ( 24) link_NAG-ASN : bond 0.00489 / 0.25 ( 6) link_NAG-ASN : angle 1.95287 / 1.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8085 (m) cc_final: 0.7796 (p) REVERT: A 525 ARG cc_start: 0.6535 (OUTLIER) cc_final: 0.6262 (mmp80) REVERT: B 150 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6486 (mm-30) REVERT: B 154 GLN cc_start: 0.7964 (mt0) cc_final: 0.7401 (mp10) outliers start: 24 outliers final: 18 residues processed: 183 average time/residue: 0.2518 time to fit residues: 60.1227 Evaluate side-chains 195 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 126 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 81 optimal weight: 0.4980 chunk 50 optimal weight: 9.9990 chunk 82 optimal weight: 0.0980 chunk 74 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 67 optimal weight: 0.2980 chunk 114 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.193319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.142757 restraints weight = 35200.908| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.40 r_work: 0.3536 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9359 Z= 0.169 Angle : 0.583 7.231 12740 Z= 0.304 Chirality : 0.046 0.345 1452 Planarity : 0.005 0.051 1654 Dihedral : 6.364 52.432 1585 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.94 % Allowed : 14.31 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.24), residues: 1154 helix: -0.60 (0.47), residues: 104 sheet: -0.64 (0.25), residues: 404 loop : -1.20 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 225 TYR 0.012 0.001 TYR A 331 PHE 0.018 0.002 PHE A 397 TRP 0.010 0.001 TRP A 115 HIS 0.004 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 9336) covalent geometry : angle 0.57206 / 0.30 (12679) SS BOND : bond 0.00250 / 0.13 ( 8) SS BOND : angle 0.67146 / 0.36 ( 16) hydrogen bonds : bond 0.03149 / 2.11 ( 295) hydrogen bonds : angle 6.33720 / 4.35 ( 774) link_ALPHA1-3 : bond 0.00583 / 0.31 ( 1) link_ALPHA1-3 : angle 1.39446 / 0.80 ( 3) link_BETA1-4 : bond 0.00569 / 0.28 ( 8) link_BETA1-4 : angle 2.08589 / 1.32 ( 24) link_NAG-ASN : bond 0.00360 / 0.19 ( 6) link_NAG-ASN : angle 1.77633 / 1.07 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8111 (m) cc_final: 0.7810 (p) REVERT: A 90 ASP cc_start: 0.7479 (p0) cc_final: 0.7263 (p0) REVERT: A 525 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.6231 (mmp80) REVERT: A 531 MET cc_start: 0.5924 (OUTLIER) cc_final: 0.5673 (pmm) REVERT: B 150 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6474 (mm-30) REVERT: B 154 GLN cc_start: 0.7993 (mt0) cc_final: 0.7398 (mp10) REVERT: C 59 VAL cc_start: 0.7655 (t) cc_final: 0.7253 (m) outliers start: 19 outliers final: 16 residues processed: 188 average time/residue: 0.2450 time to fit residues: 59.8736 Evaluate side-chains 198 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 126 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 50.0000 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 111 optimal weight: 0.1980 chunk 90 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 HIS ** 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 = 0.4322 r_free = 0.4322 target = 0.192472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.142204 restraints weight = 35034.819| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.31 r_work: 0.3534 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9359 Z= 0.244 Angle : 0.617 7.097 12740 Z= 0.323 Chirality : 0.047 0.343 1452 Planarity : 0.005 0.052 1654 Dihedral : 6.450 52.816 1585 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.35 % Allowed : 14.11 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.23), residues: 1154 helix: -0.89 (0.46), residues: 104 sheet: -0.67 (0.25), residues: 405 loop : -1.34 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 229 TYR 0.015 0.002 TYR A 220 PHE 0.024 0.002 PHE A 397 TRP 0.010 0.002 TRP A 93 HIS 0.007 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.24 ( 9336) covalent geometry : angle 0.60660 / 0.32 (12679) SS BOND : bond 0.00308 / 0.16 ( 8) SS BOND : angle 0.78592 / 0.43 ( 16) hydrogen bonds : bond 0.03396 / 2.27 ( 295) hydrogen bonds : angle 6.40160 / 4.39 ( 774) link_ALPHA1-3 : bond 0.00530 / 0.28 ( 1) link_ALPHA1-3 : angle 1.42697 / 0.82 ( 3) link_BETA1-4 : bond 0.00522 / 0.26 ( 8) link_BETA1-4 : angle 2.09673 / 1.32 ( 24) link_NAG-ASN : bond 0.00546 / 0.28 ( 6) link_NAG-ASN : angle 1.90375 / 1.14 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.284 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 48 SER cc_start: 0.8173 (m) cc_final: 0.7812 (p) REVERT: A 525 ARG cc_start: 0.6509 (OUTLIER) cc_final: 0.6235 (mmp80) REVERT: B 150 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6515 (mm-30) REVERT: B 154 GLN cc_start: 0.7979 (mt0) cc_final: 0.7413 (mp10) outliers start: 23 outliers final: 20 residues processed: 191 average time/residue: 0.2258 time to fit residues: 56.4457 Evaluate side-chains 204 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 126 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 23 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 95 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN A 210 ASN A 230 GLN ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.192970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.143246 restraints weight = 34992.542| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.31 r_work: 0.3549 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9359 Z= 0.251 Angle : 0.632 7.371 12740 Z= 0.330 Chirality : 0.047 0.343 1452 Planarity : 0.005 0.052 1654 Dihedral : 6.482 53.221 1585 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.45 % Allowed : 14.42 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.23), residues: 1154 helix: -1.00 (0.45), residues: 104 sheet: -0.69 (0.25), residues: 406 loop : -1.37 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 229 TYR 0.014 0.002 TYR A 202 PHE 0.024 0.002 PHE A 397 TRP 0.011 0.002 TRP A 93 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 ( 9336) covalent geometry : angle 0.62285 / 0.33 (12679) SS BOND : bond 0.00287 / 0.15 ( 8) SS BOND : angle 0.75761 / 0.41 ( 16) hydrogen bonds : bond 0.03414 / 2.28 ( 295) hydrogen bonds : angle 6.41301 / 4.40 ( 774) link_ALPHA1-3 : bond 0.00530 / 0.28 ( 1) link_ALPHA1-3 : angle 1.41743 / 0.81 ( 3) link_BETA1-4 : bond 0.00514 / 0.26 ( 8) link_BETA1-4 : angle 2.03966 / 1.27 ( 24) link_NAG-ASN : bond 0.00522 / 0.27 ( 6) link_NAG-ASN : angle 1.85743 / 1.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8122 (m) cc_final: 0.7777 (p) REVERT: A 122 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7793 (ttpt) REVERT: A 525 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.6259 (mmp80) REVERT: A 584 ASN cc_start: 0.6627 (OUTLIER) cc_final: 0.6300 (m-40) REVERT: B 150 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6539 (mm-30) REVERT: B 154 GLN cc_start: 0.7969 (mt0) cc_final: 0.7389 (mp10) REVERT: B 254 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7397 (mm-30) outliers start: 24 outliers final: 20 residues processed: 189 average time/residue: 0.2393 time to fit residues: 59.0620 Evaluate side-chains 199 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 126 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 81 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.191852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.141934 restraints weight = 34872.568| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.28 r_work: 0.3547 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9359 Z= 0.256 Angle : 0.634 7.311 12740 Z= 0.332 Chirality : 0.047 0.344 1452 Planarity : 0.005 0.054 1654 Dihedral : 6.473 53.290 1585 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.35 % Allowed : 14.83 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.23), residues: 1154 helix: -1.04 (0.45), residues: 104 sheet: -0.66 (0.25), residues: 407 loop : -1.40 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 229 TYR 0.022 0.002 TYR A 21 PHE 0.023 0.002 PHE A 397 TRP 0.011 0.002 TRP C 167 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.26 ( 9336) covalent geometry : angle 0.62513 / 0.33 (12679) SS BOND : bond 0.00290 / 0.15 ( 8) SS BOND : angle 0.76901 / 0.41 ( 16) hydrogen bonds : bond 0.03441 / 2.30 ( 295) hydrogen bonds : angle 6.36163 / 4.37 ( 774) link_ALPHA1-3 : bond 0.00512 / 0.27 ( 1) link_ALPHA1-3 : angle 1.42526 / 0.82 ( 3) link_BETA1-4 : bond 0.00506 / 0.25 ( 8) link_BETA1-4 : angle 2.00805 / 1.24 ( 24) link_NAG-ASN : bond 0.00514 / 0.26 ( 6) link_NAG-ASN : angle 1.82607 / 1.09 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.376 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 48 SER cc_start: 0.8097 (m) cc_final: 0.7793 (p) REVERT: A 122 LYS cc_start: 0.8055 (ttpt) cc_final: 0.7808 (ttpt) REVERT: A 525 ARG cc_start: 0.6495 (OUTLIER) cc_final: 0.6225 (mmp80) REVERT: A 584 ASN cc_start: 0.6562 (OUTLIER) cc_final: 0.6232 (m-40) REVERT: B 150 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6582 (mm-30) REVERT: B 154 GLN cc_start: 0.8012 (mt0) cc_final: 0.7449 (mp10) REVERT: B 254 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7423 (mm-30) outliers start: 23 outliers final: 21 residues processed: 191 average time/residue: 0.2313 time to fit residues: 57.8670 Evaluate side-chains 203 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 126 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 17 optimal weight: 0.0010 chunk 111 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 113 optimal weight: 0.2980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.194236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.145819 restraints weight = 35334.062| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.26 r_work: 0.3548 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9359 Z= 0.156 Angle : 0.584 7.213 12740 Z= 0.305 Chirality : 0.046 0.347 1452 Planarity : 0.005 0.049 1654 Dihedral : 6.259 52.294 1585 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.15 % Allowed : 15.24 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.24), residues: 1154 helix: -0.70 (0.46), residues: 104 sheet: -0.63 (0.25), residues: 406 loop : -1.26 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 229 TYR 0.013 0.001 TYR A 21 PHE 0.015 0.001 PHE A 397 TRP 0.010 0.001 TRP A 115 HIS 0.005 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 9336) covalent geometry : angle 0.57522 / 0.30 (12679) SS BOND : bond 0.00228 / 0.12 ( 8) SS BOND : angle 0.61835 / 0.32 ( 16) hydrogen bonds : bond 0.03021 / 2.02 ( 295) hydrogen bonds : angle 6.17562 / 4.25 ( 774) link_ALPHA1-3 : bond 0.00534 / 0.28 ( 1) link_ALPHA1-3 : angle 1.40401 / 0.80 ( 3) link_BETA1-4 : bond 0.00539 / 0.27 ( 8) link_BETA1-4 : angle 1.89186 / 1.17 ( 24) link_NAG-ASN : bond 0.00311 / 0.17 ( 6) link_NAG-ASN : angle 1.60154 / 0.96 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5088.03 seconds wall clock time: 86 minutes 40.45 seconds (5200.45 seconds total)