Starting phenix.real_space_refine on Tue Jun 10 00:06:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyf_26178/06_2025/7tyf_26178.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyf_26178/06_2025/7tyf_26178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyf_26178/06_2025/7tyf_26178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyf_26178/06_2025/7tyf_26178.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyf_26178/06_2025/7tyf_26178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyf_26178/06_2025/7tyf_26178.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 P 2 5.49 5 S 71 5.16 5 C 6599 2.51 5 N 1730 2.21 5 O 1929 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10331 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1857 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "E" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 759 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 6, 'TRANS': 105} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 87 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 284 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Conformer: "B" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} bond proxies already assigned to first conformer: 265 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2982 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "R" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 362 Unusual residues: {'NAG': 2, 'P42': 1, 'PLM': 9, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "P" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG P 18 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG P 18 " occ=0.50 Time building chain proxies: 7.50, per 1000 atoms: 0.73 Number of scatterers: 10331 At special positions: 0 Unit cell: (109.56, 98.77, 151.06, 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 71 16.00 P 2 15.00 O 1929 8.00 N 1730 7.00 C 6599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.04 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.04 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " 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=1, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 73 " " NAG R 502 " - " ASN R 130 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.3 seconds 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 13 sheets defined 45.5% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 11 through 40 removed outlier: 3.564A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.945A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.533A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.830A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.627A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 34 through 48 removed outlier: 4.338A pdb=" N CYS E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 41 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 81 removed outlier: 3.748A pdb=" N ARG E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA E 70 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS E 79 " --> pdb=" O HIS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 100 Processing helix chain 'E' and resid 115 through 143 Proline residue: E 121 - end of helix Proline residue: E 126 - end of helix removed outlier: 3.509A pdb=" N ARG E 143 " --> pdb=" O TRP E 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.500A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 19 Processing helix chain 'R' and resid 44 through 62 removed outlier: 3.628A pdb=" N MET R 48 " --> pdb=" O GLY R 44 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP R 57 " --> pdb=" O TYR R 53 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU R 62 " --> pdb=" O ARG R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 137 removed outlier: 4.512A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE R 137 " --> pdb=" O MET R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.547A pdb=" N ASN R 144 " --> pdb=" O GLU R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 204 Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.577A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.689A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 405 Processing helix chain 'R' and resid 406 through 409 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.464A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.875A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.814A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.746A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.685A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.639A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.537A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.707A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.114A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 71 through 72 removed outlier: 3.562A pdb=" N CYS R 72 " --> pdb=" O THR R 85 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR R 85 " --> pdb=" O CYS R 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'R' and resid 90 through 94 528 hydrogen bonds defined for protein. 1489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1691 1.32 - 1.45: 2895 1.45 - 1.58: 5789 1.58 - 1.70: 4 1.70 - 1.83: 99 Bond restraints: 10478 Sorted by residual: bond pdb=" N ILE E 106 " pdb=" CA ILE E 106 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.26e-02 6.30e+03 8.20e+00 bond pdb=" N ASP E 58 " pdb=" CA ASP E 58 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.22e-02 6.72e+03 6.95e+00 bond pdb=" N THR E 54 " pdb=" CA THR E 54 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.53e+00 bond pdb=" OBN P42 R 510 " pdb=" PBM P42 R 510 " ideal model delta sigma weight residual 1.657 1.607 0.050 2.00e-02 2.50e+03 6.36e+00 bond pdb=" N SER E 103 " pdb=" CA SER E 103 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.17e-02 7.31e+03 6.15e+00 ... (remaining 10473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 13960 1.90 - 3.81: 184 3.81 - 5.71: 19 5.71 - 7.62: 1 7.62 - 9.52: 2 Bond angle restraints: 14166 Sorted by residual: angle pdb=" N ILE E 118 " pdb=" CA ILE E 118 " pdb=" C ILE E 118 " ideal model delta sigma weight residual 112.96 109.64 3.32 1.00e+00 1.00e+00 1.10e+01 angle pdb=" N VAL B 90 " pdb=" CA VAL B 90 " pdb=" C VAL B 90 " ideal model delta sigma weight residual 111.81 109.07 2.74 8.60e-01 1.35e+00 1.02e+01 angle pdb=" O11 PTY R 514 " pdb=" P1 PTY R 514 " pdb=" O14 PTY R 514 " ideal model delta sigma weight residual 92.90 102.42 -9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" N THR E 54 " pdb=" CA THR E 54 " pdb=" C THR E 54 " ideal model delta sigma weight residual 113.16 109.37 3.79 1.24e+00 6.50e-01 9.34e+00 angle pdb=" CA LEU E 55 " pdb=" C LEU E 55 " pdb=" O LEU E 55 " ideal model delta sigma weight residual 120.55 117.60 2.95 1.06e+00 8.90e-01 7.72e+00 ... (remaining 14161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.66: 6089 26.66 - 53.32: 241 53.32 - 79.98: 48 79.98 - 106.64: 4 106.64 - 133.30: 2 Dihedral angle restraints: 6384 sinusoidal: 2692 harmonic: 3692 Sorted by residual: dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual -86.00 -21.95 -64.05 1 1.00e+01 1.00e-02 5.40e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual 93.00 147.10 -54.10 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 6381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1140 0.041 - 0.082: 313 0.082 - 0.123: 96 0.123 - 0.164: 6 0.164 - 0.204: 3 Chirality restraints: 1558 Sorted by residual: chirality pdb=" CBE P42 R 510 " pdb=" CAB P42 R 510 " pdb=" CBK P42 R 510 " pdb=" OBD P42 R 510 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE E 106 " pdb=" N ILE E 106 " pdb=" C ILE E 106 " pdb=" CB ILE E 106 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" C1 NAG R 502 " pdb=" ND2 ASN R 130 " pdb=" C2 NAG R 502 " pdb=" O5 NAG R 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.31e-01 ... (remaining 1555 not shown) Planarity restraints: 1777 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN R 73 " -0.016 2.00e-02 2.50e+03 1.48e-02 2.72e+00 pdb=" CG ASN R 73 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN R 73 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN R 73 " 0.011 2.00e-02 2.50e+03 pdb=" C1 NAG R 501 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.88e+00 pdb=" N PRO B 236 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 303 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.84e+00 pdb=" N PRO R 304 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO R 304 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 304 " -0.019 5.00e-02 4.00e+02 ... (remaining 1774 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1828 2.77 - 3.30: 9967 3.30 - 3.83: 18014 3.83 - 4.37: 22208 4.37 - 4.90: 36257 Nonbonded interactions: 88274 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.234 3.040 nonbonded pdb=" O LEU P 16 " pdb=" OG SER P 20 " model vdw 2.274 3.040 nonbonded pdb=" O TYR A 318 " pdb=" NH1 ARG A 336 " model vdw 2.292 3.120 nonbonded pdb=" OD1 ASP N 106 " pdb=" O HOH N 201 " model vdw 2.294 3.040 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.300 3.120 ... (remaining 88269 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=0.50 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: 0.010 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 26.820 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 10490 Z= 0.232 Angle : 0.576 9.523 14190 Z= 0.325 Chirality : 0.042 0.204 1558 Planarity : 0.003 0.034 1775 Dihedral : 14.565 133.305 3973 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.87 % Allowed : 10.84 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.20), residues: 1251 helix: -1.23 (0.18), residues: 503 sheet: -0.21 (0.32), residues: 226 loop : -1.32 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.005 0.001 HIS A 41 PHE 0.012 0.001 PHE B 151 TYR 0.009 0.001 TYR R 65 ARG 0.004 0.000 ARG R 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00934 ( 2) link_NAG-ASN : angle 3.05914 ( 6) hydrogen bonds : bond 0.22690 ( 528) hydrogen bonds : angle 7.85798 ( 1489) SS BOND : bond 0.00351 ( 9) SS BOND : angle 0.92906 ( 18) covalent geometry : bond 0.00389 (10478) covalent geometry : angle 0.57163 (14166) Misc. bond : bond 0.10594 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 1.182 Fit side-chains REVERT: A 370 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6604 (tp30) REVERT: B 19 ARG cc_start: 0.7556 (ttp-110) cc_final: 0.7274 (ttm-80) REVERT: B 197 ARG cc_start: 0.7610 (mmm-85) cc_final: 0.7326 (mmm160) REVERT: B 214 ARG cc_start: 0.7199 (mmt180) cc_final: 0.6854 (mmt180) REVERT: P 23 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5881 (mp) REVERT: R 130 ASN cc_start: 0.3481 (OUTLIER) cc_final: 0.2829 (t0) REVERT: R 167 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7956 (tt) REVERT: R 328 ARG cc_start: 0.6994 (mtt180) cc_final: 0.6526 (mtt-85) outliers start: 9 outliers final: 4 residues processed: 193 average time/residue: 1.4945 time to fit residues: 306.1199 Evaluate side-chains 172 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain R residue 167 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 294 GLN B 16 ASN B 32 GLN B 75 GLN B 88 ASN B 155 ASN N 3 GLN N 13 GLN N 77 ASN P 22 ASN R 201 HIS R 318 ASN R 365 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.194142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.154225 restraints weight = 18576.359| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.79 r_work: 0.3056 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10490 Z= 0.154 Angle : 0.577 7.552 14190 Z= 0.313 Chirality : 0.044 0.148 1558 Planarity : 0.004 0.041 1775 Dihedral : 9.097 99.839 1794 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.42 % Allowed : 12.78 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.23), residues: 1251 helix: 0.97 (0.22), residues: 516 sheet: -0.17 (0.32), residues: 239 loop : -0.99 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 PHE 0.013 0.001 PHE B 151 TYR 0.022 0.002 TYR R 56 ARG 0.005 0.001 ARG B 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 2) link_NAG-ASN : angle 1.51792 ( 6) hydrogen bonds : bond 0.05916 ( 528) hydrogen bonds : angle 5.13185 ( 1489) SS BOND : bond 0.00364 ( 9) SS BOND : angle 0.99486 ( 18) covalent geometry : bond 0.00315 (10478) covalent geometry : angle 0.57556 (14166) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7154 (mtm-85) cc_final: 0.6492 (mpt180) REVERT: A 31 GLN cc_start: 0.8157 (tp40) cc_final: 0.7945 (tp40) REVERT: A 370 GLU cc_start: 0.7604 (mm-30) cc_final: 0.6956 (mp0) REVERT: B 19 ARG cc_start: 0.7875 (ttp-110) cc_final: 0.7349 (ttm-80) REVERT: B 44 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6628 (pt0) REVERT: B 197 ARG cc_start: 0.8363 (mmm-85) cc_final: 0.7762 (mmm160) REVERT: B 214 ARG cc_start: 0.7484 (mmt180) cc_final: 0.7062 (mmt180) REVERT: G 13 ARG cc_start: 0.6464 (ttm170) cc_final: 0.6218 (ttm110) REVERT: R 140 GLU cc_start: 0.6367 (mm-30) cc_final: 0.5958 (mp0) REVERT: R 171 VAL cc_start: 0.7422 (t) cc_final: 0.7088 (m) REVERT: R 174 ARG cc_start: 0.6476 (mtp180) cc_final: 0.6262 (mtp180) REVERT: R 258 ARG cc_start: 0.7031 (mtm180) cc_final: 0.6223 (mtt-85) REVERT: R 321 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7811 (ttt-90) REVERT: R 328 ARG cc_start: 0.7330 (mtt180) cc_final: 0.6859 (mtt-85) REVERT: R 343 LYS cc_start: 0.8102 (tttt) cc_final: 0.7535 (tmmt) outliers start: 25 outliers final: 12 residues processed: 197 average time/residue: 1.4418 time to fit residues: 301.9029 Evaluate side-chains 182 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 85 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 64 optimal weight: 0.0670 chunk 10 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 91 HIS E 140 GLN N 3 GLN N 13 GLN N 77 ASN R 257 GLN R 365 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.196819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.156434 restraints weight = 17527.787| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.91 r_work: 0.3115 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10490 Z= 0.109 Angle : 0.510 7.549 14190 Z= 0.272 Chirality : 0.041 0.158 1558 Planarity : 0.004 0.041 1775 Dihedral : 7.962 74.895 1787 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.03 % Allowed : 13.07 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1251 helix: 1.87 (0.23), residues: 509 sheet: -0.06 (0.33), residues: 232 loop : -0.65 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 381 PHE 0.013 0.001 PHE R 161 TYR 0.021 0.001 TYR R 56 ARG 0.002 0.000 ARG B 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 2) link_NAG-ASN : angle 1.11258 ( 6) hydrogen bonds : bond 0.04548 ( 528) hydrogen bonds : angle 4.63551 ( 1489) SS BOND : bond 0.00230 ( 9) SS BOND : angle 0.73843 ( 18) covalent geometry : bond 0.00217 (10478) covalent geometry : angle 0.50887 (14166) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7013 (mtm-85) cc_final: 0.6454 (mpt180) REVERT: A 27 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7812 (mm-30) REVERT: A 35 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7352 (mm110) REVERT: A 300 LYS cc_start: 0.5041 (mmmm) cc_final: 0.4746 (mttm) REVERT: A 370 GLU cc_start: 0.7542 (mm-30) cc_final: 0.6897 (mp0) REVERT: B 12 GLU cc_start: 0.6987 (tp30) cc_final: 0.6551 (tt0) REVERT: B 15 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7381 (mtpm) REVERT: B 16 ASN cc_start: 0.7648 (m-40) cc_final: 0.7441 (m110) REVERT: B 19 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7310 (ttm-80) REVERT: B 44 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6548 (pt0) REVERT: B 197 ARG cc_start: 0.8299 (mmm-85) cc_final: 0.7733 (mmm160) REVERT: B 214 ARG cc_start: 0.7454 (mmt180) cc_final: 0.7036 (mmt180) REVERT: B 304 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7887 (ttp-170) REVERT: R 140 GLU cc_start: 0.6151 (mm-30) cc_final: 0.5759 (mp0) REVERT: R 171 VAL cc_start: 0.7382 (t) cc_final: 0.7082 (m) REVERT: R 174 ARG cc_start: 0.6480 (mtp180) cc_final: 0.6104 (mtp180) REVERT: R 254 THR cc_start: 0.7116 (m) cc_final: 0.6598 (p) REVERT: R 328 ARG cc_start: 0.7220 (mtt180) cc_final: 0.6745 (mtt-85) REVERT: R 343 LYS cc_start: 0.8080 (tttt) cc_final: 0.7513 (tmmt) outliers start: 21 outliers final: 8 residues processed: 188 average time/residue: 1.4965 time to fit residues: 298.8387 Evaluate side-chains 175 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain R residue 130 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 64 optimal weight: 0.1980 chunk 74 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN E 140 GLN N 3 GLN N 13 GLN R 257 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.196435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.135955 restraints weight = 10858.386| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.70 r_work: 0.3240 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10490 Z= 0.112 Angle : 0.514 7.896 14190 Z= 0.274 Chirality : 0.041 0.169 1558 Planarity : 0.004 0.042 1775 Dihedral : 7.722 75.375 1787 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.13 % Allowed : 13.84 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.24), residues: 1251 helix: 2.04 (0.23), residues: 515 sheet: -0.04 (0.32), residues: 237 loop : -0.64 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 234 HIS 0.003 0.001 HIS R 302 PHE 0.014 0.001 PHE R 161 TYR 0.018 0.001 TYR R 56 ARG 0.007 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 2) link_NAG-ASN : angle 1.14686 ( 6) hydrogen bonds : bond 0.04431 ( 528) hydrogen bonds : angle 4.53337 ( 1489) SS BOND : bond 0.00271 ( 9) SS BOND : angle 0.78612 ( 18) covalent geometry : bond 0.00225 (10478) covalent geometry : angle 0.51335 (14166) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6994 (mtm-85) cc_final: 0.6391 (mpt180) REVERT: A 27 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7624 (mm-30) REVERT: A 35 GLN cc_start: 0.7589 (tm-30) cc_final: 0.7248 (mm110) REVERT: A 296 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6616 (mp) REVERT: A 300 LYS cc_start: 0.5082 (mmmm) cc_final: 0.4849 (mttm) REVERT: A 370 GLU cc_start: 0.7459 (mm-30) cc_final: 0.6797 (mp0) REVERT: B 12 GLU cc_start: 0.6930 (tp30) cc_final: 0.6517 (tt0) REVERT: B 15 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7173 (mtpm) REVERT: B 16 ASN cc_start: 0.7497 (m-40) cc_final: 0.7292 (m110) REVERT: B 19 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.7122 (ttm-80) REVERT: B 44 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6588 (pt0) REVERT: B 197 ARG cc_start: 0.8270 (mmm-85) cc_final: 0.7656 (mmm160) REVERT: B 212 ASP cc_start: 0.8736 (t70) cc_final: 0.8531 (t70) REVERT: B 214 ARG cc_start: 0.7441 (mmt180) cc_final: 0.7004 (mmt180) REVERT: E 40 CYS cc_start: 0.2526 (OUTLIER) cc_final: 0.1935 (p) REVERT: R 90 LEU cc_start: 0.2165 (OUTLIER) cc_final: 0.1203 (pt) REVERT: R 130 ASN cc_start: 0.3176 (OUTLIER) cc_final: 0.2612 (t0) REVERT: R 140 GLU cc_start: 0.5983 (mm-30) cc_final: 0.5639 (mp0) REVERT: R 171 VAL cc_start: 0.7296 (t) cc_final: 0.6964 (m) REVERT: R 174 ARG cc_start: 0.6427 (mtp180) cc_final: 0.6043 (mtp180) REVERT: R 254 THR cc_start: 0.7103 (m) cc_final: 0.6580 (p) REVERT: R 328 ARG cc_start: 0.7087 (mtt180) cc_final: 0.6598 (mtt-85) REVERT: R 343 LYS cc_start: 0.7970 (tttt) cc_final: 0.7340 (tmmt) REVERT: R 364 SER cc_start: 0.8073 (m) cc_final: 0.7279 (p) outliers start: 22 outliers final: 12 residues processed: 184 average time/residue: 1.5294 time to fit residues: 299.3661 Evaluate side-chains 180 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain R residue 327 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 41 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS B 340 ASN E 140 GLN N 13 GLN R 208 ASN R 257 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.194834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.153131 restraints weight = 20683.533| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.18 r_work: 0.3072 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10490 Z= 0.136 Angle : 0.554 7.891 14190 Z= 0.295 Chirality : 0.043 0.177 1558 Planarity : 0.004 0.042 1775 Dihedral : 7.954 75.120 1787 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.61 % Allowed : 14.52 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.24), residues: 1251 helix: 2.05 (0.23), residues: 515 sheet: -0.03 (0.32), residues: 237 loop : -0.59 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 PHE 0.013 0.001 PHE R 161 TYR 0.020 0.002 TYR R 56 ARG 0.006 0.001 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 2) link_NAG-ASN : angle 1.19336 ( 6) hydrogen bonds : bond 0.04832 ( 528) hydrogen bonds : angle 4.62737 ( 1489) SS BOND : bond 0.00357 ( 9) SS BOND : angle 0.98415 ( 18) covalent geometry : bond 0.00280 (10478) covalent geometry : angle 0.55235 (14166) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7156 (mtm-85) cc_final: 0.6556 (mpt180) REVERT: A 35 GLN cc_start: 0.7655 (tm-30) cc_final: 0.7336 (mm110) REVERT: A 296 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6569 (mp) REVERT: A 300 LYS cc_start: 0.4977 (OUTLIER) cc_final: 0.4709 (mttm) REVERT: A 370 GLU cc_start: 0.7582 (mm-30) cc_final: 0.6758 (tp30) REVERT: B 12 GLU cc_start: 0.7018 (tp30) cc_final: 0.6566 (tt0) REVERT: B 19 ARG cc_start: 0.7830 (ttp-110) cc_final: 0.7259 (ttm-80) REVERT: B 44 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6645 (pt0) REVERT: B 137 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8301 (tpp-160) REVERT: B 197 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.7713 (mmm160) REVERT: B 214 ARG cc_start: 0.7496 (mmt180) cc_final: 0.7033 (mmt180) REVERT: E 40 CYS cc_start: 0.2515 (OUTLIER) cc_final: 0.1977 (p) REVERT: G 13 ARG cc_start: 0.6285 (ttm170) cc_final: 0.5963 (ttm110) REVERT: R 48 MET cc_start: 0.4455 (ptp) cc_final: 0.3380 (ttt) REVERT: R 90 LEU cc_start: 0.2206 (OUTLIER) cc_final: 0.1214 (pt) REVERT: R 130 ASN cc_start: 0.3398 (OUTLIER) cc_final: 0.2743 (t0) REVERT: R 140 GLU cc_start: 0.6018 (mm-30) cc_final: 0.5660 (mp0) REVERT: R 171 VAL cc_start: 0.7345 (t) cc_final: 0.7001 (m) REVERT: R 174 ARG cc_start: 0.6459 (mtp180) cc_final: 0.6211 (mtp180) REVERT: R 208 ASN cc_start: 0.6265 (OUTLIER) cc_final: 0.6020 (t0) REVERT: R 254 THR cc_start: 0.6959 (m) cc_final: 0.6448 (p) REVERT: R 264 LEU cc_start: 0.8002 (tp) cc_final: 0.7691 (mt) REVERT: R 328 ARG cc_start: 0.7208 (mtt180) cc_final: 0.6708 (mtt-85) REVERT: R 343 LYS cc_start: 0.8046 (tttt) cc_final: 0.7442 (tmmt) REVERT: R 364 SER cc_start: 0.8087 (m) cc_final: 0.7300 (p) REVERT: R 367 MET cc_start: 0.5331 (tmm) cc_final: 0.5081 (tmm) outliers start: 27 outliers final: 15 residues processed: 186 average time/residue: 1.5189 time to fit residues: 300.1730 Evaluate side-chains 189 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain R residue 208 ASN Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 347 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 80 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 266 HIS B 340 ASN E 140 GLN N 13 GLN R 208 ASN R 257 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.194726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.146137 restraints weight = 18084.384| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 4.66 r_work: 0.3084 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10490 Z= 0.136 Angle : 0.557 8.346 14190 Z= 0.296 Chirality : 0.043 0.182 1558 Planarity : 0.004 0.041 1775 Dihedral : 7.996 75.459 1787 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.81 % Allowed : 14.52 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.24), residues: 1251 helix: 2.08 (0.23), residues: 515 sheet: -0.04 (0.32), residues: 237 loop : -0.59 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.004 0.001 HIS A 41 PHE 0.013 0.001 PHE B 151 TYR 0.012 0.001 TYR P 37 ARG 0.008 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 2) link_NAG-ASN : angle 1.31630 ( 6) hydrogen bonds : bond 0.04793 ( 528) hydrogen bonds : angle 4.60684 ( 1489) SS BOND : bond 0.00356 ( 9) SS BOND : angle 1.09605 ( 18) covalent geometry : bond 0.00282 (10478) covalent geometry : angle 0.55528 (14166) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7093 (mtm-85) cc_final: 0.6486 (mpt180) REVERT: A 27 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7678 (tp30) REVERT: A 35 GLN cc_start: 0.7600 (tm-30) cc_final: 0.7280 (mm110) REVERT: A 296 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6532 (mp) REVERT: A 300 LYS cc_start: 0.5011 (OUTLIER) cc_final: 0.4711 (mttm) REVERT: A 370 GLU cc_start: 0.7526 (mm-30) cc_final: 0.6724 (OUTLIER) REVERT: B 12 GLU cc_start: 0.6948 (tp30) cc_final: 0.6499 (tt0) REVERT: B 19 ARG cc_start: 0.7756 (ttp-110) cc_final: 0.7171 (ttm-80) REVERT: B 44 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6608 (pt0) REVERT: B 137 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8260 (tpp-160) REVERT: B 197 ARG cc_start: 0.8321 (mmm-85) cc_final: 0.7681 (mmm160) REVERT: B 214 ARG cc_start: 0.7419 (mmt180) cc_final: 0.6953 (mmt180) REVERT: E 40 CYS cc_start: 0.2625 (OUTLIER) cc_final: 0.2060 (p) REVERT: G 13 ARG cc_start: 0.6255 (ttm170) cc_final: 0.5925 (ttm110) REVERT: G 38 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8112 (ptt) REVERT: G 46 LYS cc_start: 0.7837 (mttt) cc_final: 0.7595 (mmtm) REVERT: R 48 MET cc_start: 0.4307 (ptp) cc_final: 0.3335 (ttt) REVERT: R 90 LEU cc_start: 0.2212 (OUTLIER) cc_final: 0.1278 (pt) REVERT: R 130 ASN cc_start: 0.3384 (OUTLIER) cc_final: 0.2656 (t0) REVERT: R 140 GLU cc_start: 0.6011 (mm-30) cc_final: 0.5603 (mp0) REVERT: R 171 VAL cc_start: 0.7256 (t) cc_final: 0.6909 (m) REVERT: R 174 ARG cc_start: 0.6411 (mtp180) cc_final: 0.6150 (mtp180) REVERT: R 208 ASN cc_start: 0.5777 (OUTLIER) cc_final: 0.5512 (p0) REVERT: R 254 THR cc_start: 0.6969 (m) cc_final: 0.6454 (p) REVERT: R 264 LEU cc_start: 0.7939 (tp) cc_final: 0.7629 (mt) REVERT: R 328 ARG cc_start: 0.7221 (mtt180) cc_final: 0.6726 (mtt-85) REVERT: R 343 LYS cc_start: 0.7978 (tttt) cc_final: 0.7348 (tmmt) REVERT: R 364 SER cc_start: 0.8080 (m) cc_final: 0.7281 (p) REVERT: R 367 MET cc_start: 0.5330 (tmm) cc_final: 0.5105 (tmm) outliers start: 29 outliers final: 18 residues processed: 190 average time/residue: 1.5349 time to fit residues: 309.4413 Evaluate side-chains 196 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain R residue 208 ASN Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 347 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 8 optimal weight: 0.0370 chunk 42 optimal weight: 4.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 17 GLN B 266 HIS B 340 ASN E 140 GLN N 13 GLN R 208 ASN R 257 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.195882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.163021 restraints weight = 16217.705| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.18 r_work: 0.3110 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10490 Z= 0.116 Angle : 0.533 8.452 14190 Z= 0.282 Chirality : 0.042 0.189 1558 Planarity : 0.004 0.041 1775 Dihedral : 7.820 75.964 1787 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.71 % Allowed : 14.91 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.24), residues: 1251 helix: 2.22 (0.23), residues: 515 sheet: 0.06 (0.32), residues: 241 loop : -0.58 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 234 HIS 0.003 0.001 HIS A 41 PHE 0.012 0.001 PHE B 151 TYR 0.012 0.001 TYR R 56 ARG 0.007 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 2) link_NAG-ASN : angle 1.20957 ( 6) hydrogen bonds : bond 0.04444 ( 528) hydrogen bonds : angle 4.49313 ( 1489) SS BOND : bond 0.00313 ( 9) SS BOND : angle 0.94586 ( 18) covalent geometry : bond 0.00236 (10478) covalent geometry : angle 0.53190 (14166) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7142 (mtm-85) cc_final: 0.6620 (mpt180) REVERT: A 27 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7738 (tp30) REVERT: A 35 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7367 (mm110) REVERT: A 296 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6638 (mp) REVERT: A 370 GLU cc_start: 0.7577 (mm-30) cc_final: 0.6813 (tp30) REVERT: B 12 GLU cc_start: 0.7011 (tp30) cc_final: 0.6604 (tt0) REVERT: B 19 ARG cc_start: 0.7846 (ttp-110) cc_final: 0.7337 (ttm-80) REVERT: B 44 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6632 (pt0) REVERT: B 137 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8245 (tpp-160) REVERT: B 197 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.7805 (mmm160) REVERT: B 214 ARG cc_start: 0.7443 (mmt180) cc_final: 0.6975 (mmt180) REVERT: B 215 GLU cc_start: 0.7692 (mp0) cc_final: 0.7442 (mm-30) REVERT: B 304 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7878 (ttp-170) REVERT: E 40 CYS cc_start: 0.2433 (OUTLIER) cc_final: 0.1969 (p) REVERT: G 13 ARG cc_start: 0.6332 (ttm170) cc_final: 0.5991 (ttm110) REVERT: G 38 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8097 (ptt) REVERT: R 48 MET cc_start: 0.4384 (ptp) cc_final: 0.3499 (ttt) REVERT: R 90 LEU cc_start: 0.2419 (OUTLIER) cc_final: 0.1445 (pt) REVERT: R 130 ASN cc_start: 0.3495 (OUTLIER) cc_final: 0.2739 (t0) REVERT: R 140 GLU cc_start: 0.6080 (mm-30) cc_final: 0.5706 (mp0) REVERT: R 171 VAL cc_start: 0.7312 (t) cc_final: 0.6951 (m) REVERT: R 174 ARG cc_start: 0.6469 (mtp180) cc_final: 0.6227 (mtp180) REVERT: R 254 THR cc_start: 0.6995 (m) cc_final: 0.6498 (p) REVERT: R 264 LEU cc_start: 0.7973 (tp) cc_final: 0.7693 (mt) REVERT: R 328 ARG cc_start: 0.7212 (mtt180) cc_final: 0.6730 (mtt-85) REVERT: R 343 LYS cc_start: 0.8057 (tttt) cc_final: 0.7486 (tmmt) REVERT: R 364 SER cc_start: 0.8045 (m) cc_final: 0.7252 (p) REVERT: R 367 MET cc_start: 0.5325 (tmm) cc_final: 0.5089 (tmm) outliers start: 28 outliers final: 14 residues processed: 193 average time/residue: 1.4953 time to fit residues: 306.5323 Evaluate side-chains 187 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 130 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 91 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.0870 chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 39 optimal weight: 0.0970 chunk 112 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 overall best weight: 1.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 17 GLN B 266 HIS B 340 ASN N 13 GLN N 35 ASN R 257 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.195045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.146440 restraints weight = 11847.212| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.19 r_work: 0.3249 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10490 Z= 0.134 Angle : 0.564 8.585 14190 Z= 0.300 Chirality : 0.043 0.197 1558 Planarity : 0.004 0.042 1775 Dihedral : 8.009 76.240 1787 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.10 % Allowed : 14.81 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.24), residues: 1251 helix: 2.19 (0.23), residues: 515 sheet: 0.08 (0.32), residues: 241 loop : -0.56 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.004 0.001 HIS A 41 PHE 0.013 0.001 PHE R 269 TYR 0.013 0.001 TYR R 56 ARG 0.007 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 2) link_NAG-ASN : angle 1.32791 ( 6) hydrogen bonds : bond 0.04679 ( 528) hydrogen bonds : angle 4.57214 ( 1489) SS BOND : bond 0.00359 ( 9) SS BOND : angle 1.01236 ( 18) covalent geometry : bond 0.00275 (10478) covalent geometry : angle 0.56271 (14166) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7153 (mtm-85) cc_final: 0.6621 (mpt180) REVERT: A 27 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7870 (tp30) REVERT: A 35 GLN cc_start: 0.7649 (tm-30) cc_final: 0.7436 (mm110) REVERT: A 296 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6712 (mp) REVERT: A 370 GLU cc_start: 0.7575 (mm-30) cc_final: 0.6775 (OUTLIER) REVERT: B 9 GLN cc_start: 0.6565 (OUTLIER) cc_final: 0.6151 (mt0) REVERT: B 12 GLU cc_start: 0.6935 (tp30) cc_final: 0.6548 (tt0) REVERT: B 19 ARG cc_start: 0.7807 (ttp-110) cc_final: 0.7273 (ttm-80) REVERT: B 44 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6610 (pt0) REVERT: B 137 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8119 (tpp-160) REVERT: B 197 ARG cc_start: 0.8332 (mmm-85) cc_final: 0.7803 (mmm160) REVERT: B 214 ARG cc_start: 0.7378 (mmt180) cc_final: 0.6897 (mmt180) REVERT: B 215 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7306 (mm-30) REVERT: E 40 CYS cc_start: 0.2476 (OUTLIER) cc_final: 0.1970 (p) REVERT: G 13 ARG cc_start: 0.6263 (ttm170) cc_final: 0.5948 (ttm110) REVERT: G 38 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8110 (ptt) REVERT: R 48 MET cc_start: 0.4350 (ptp) cc_final: 0.3472 (ttt) REVERT: R 90 LEU cc_start: 0.2402 (OUTLIER) cc_final: 0.1434 (pt) REVERT: R 140 GLU cc_start: 0.6052 (mm-30) cc_final: 0.5704 (mp0) REVERT: R 171 VAL cc_start: 0.7265 (t) cc_final: 0.6907 (m) REVERT: R 174 ARG cc_start: 0.6401 (mtp180) cc_final: 0.6160 (mtp180) REVERT: R 254 THR cc_start: 0.7106 (m) cc_final: 0.6622 (p) REVERT: R 264 LEU cc_start: 0.7952 (tp) cc_final: 0.7681 (mt) REVERT: R 328 ARG cc_start: 0.7194 (mtt180) cc_final: 0.6706 (mtt-85) REVERT: R 343 LYS cc_start: 0.8011 (tttt) cc_final: 0.7433 (tmmt) REVERT: R 364 SER cc_start: 0.8049 (m) cc_final: 0.7246 (p) REVERT: R 367 MET cc_start: 0.5303 (tmm) cc_final: 0.5065 (tmm) REVERT: R 368 LEU cc_start: 0.7091 (mt) cc_final: 0.6779 (tp) outliers start: 32 outliers final: 19 residues processed: 189 average time/residue: 1.5811 time to fit residues: 317.2209 Evaluate side-chains 193 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 349 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 98 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 32 GLN B 266 HIS B 340 ASN N 13 GLN N 35 ASN R 257 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.193313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.148476 restraints weight = 15005.245| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.46 r_work: 0.3056 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10490 Z= 0.181 Angle : 0.686 24.713 14190 Z= 0.349 Chirality : 0.052 0.938 1558 Planarity : 0.005 0.060 1775 Dihedral : 9.070 76.462 1785 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.00 % Allowed : 14.91 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.24), residues: 1251 helix: 1.95 (0.23), residues: 516 sheet: 0.02 (0.32), residues: 244 loop : -0.60 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.007 0.002 HIS B 225 PHE 0.016 0.002 PHE R 269 TYR 0.014 0.002 TYR P 37 ARG 0.010 0.001 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.01389 ( 2) link_NAG-ASN : angle 11.73591 ( 6) hydrogen bonds : bond 0.05353 ( 528) hydrogen bonds : angle 4.79260 ( 1489) SS BOND : bond 0.00491 ( 9) SS BOND : angle 1.28711 ( 18) covalent geometry : bond 0.00383 (10478) covalent geometry : angle 0.64136 (14166) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.079 Fit side-chains REVERT: A 27 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7848 (tp30) REVERT: A 296 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6611 (mp) REVERT: A 370 GLU cc_start: 0.7608 (mm-30) cc_final: 0.6775 (tp30) REVERT: B 9 GLN cc_start: 0.6476 (OUTLIER) cc_final: 0.6093 (mt0) REVERT: B 12 GLU cc_start: 0.7005 (tp30) cc_final: 0.6569 (tt0) REVERT: B 19 ARG cc_start: 0.7781 (ttp-110) cc_final: 0.7187 (ttm-80) REVERT: B 44 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6662 (pt0) REVERT: B 197 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.7791 (mmm160) REVERT: B 214 ARG cc_start: 0.7515 (mmt180) cc_final: 0.6940 (mmt180) REVERT: B 215 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7390 (mm-30) REVERT: B 304 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7926 (ttp-170) REVERT: B 340 ASN cc_start: 0.7857 (t0) cc_final: 0.7651 (t160) REVERT: E 40 CYS cc_start: 0.2485 (OUTLIER) cc_final: 0.1913 (p) REVERT: G 13 ARG cc_start: 0.6356 (ttm170) cc_final: 0.6026 (ttm110) REVERT: R 48 MET cc_start: 0.4278 (ptp) cc_final: 0.3453 (ttt) REVERT: R 90 LEU cc_start: 0.2274 (OUTLIER) cc_final: 0.1330 (pt) REVERT: R 120 LYS cc_start: 0.5317 (OUTLIER) cc_final: 0.4980 (mmtm) REVERT: R 140 GLU cc_start: 0.6164 (mm-30) cc_final: 0.5733 (mp0) REVERT: R 171 VAL cc_start: 0.7321 (t) cc_final: 0.6978 (m) REVERT: R 254 THR cc_start: 0.7096 (m) cc_final: 0.6530 (p) REVERT: R 264 LEU cc_start: 0.7989 (tp) cc_final: 0.7697 (mt) REVERT: R 328 ARG cc_start: 0.7260 (mtt180) cc_final: 0.6736 (mtt-85) REVERT: R 343 LYS cc_start: 0.8008 (tttt) cc_final: 0.7386 (tmmt) REVERT: R 364 SER cc_start: 0.8102 (m) cc_final: 0.7362 (p) REVERT: R 367 MET cc_start: 0.5356 (tmm) cc_final: 0.5058 (tmm) REVERT: R 368 LEU cc_start: 0.7066 (mt) cc_final: 0.6762 (tp) outliers start: 31 outliers final: 16 residues processed: 188 average time/residue: 1.5407 time to fit residues: 307.8845 Evaluate side-chains 191 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 349 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 88 optimal weight: 0.0980 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 17 GLN B 266 HIS N 13 GLN N 35 ASN R 257 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.196990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.153688 restraints weight = 15039.379| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.35 r_work: 0.3114 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10490 Z= 0.110 Angle : 0.580 20.306 14190 Z= 0.293 Chirality : 0.046 0.736 1558 Planarity : 0.003 0.040 1775 Dihedral : 8.400 76.211 1785 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.23 % Allowed : 15.59 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.24), residues: 1251 helix: 2.35 (0.23), residues: 509 sheet: 0.04 (0.32), residues: 236 loop : -0.46 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 41 PHE 0.013 0.001 PHE B 151 TYR 0.014 0.001 TYR R 56 ARG 0.009 0.000 ARG B 219 Details of bonding type rmsd link_NAG-ASN : bond 0.01200 ( 2) link_NAG-ASN : angle 9.53002 ( 6) hydrogen bonds : bond 0.04204 ( 528) hydrogen bonds : angle 4.44894 ( 1489) SS BOND : bond 0.00392 ( 9) SS BOND : angle 0.93517 ( 18) covalent geometry : bond 0.00223 (10478) covalent geometry : angle 0.54577 (14166) Misc. bond : bond 0.00033 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7052 (mtm-85) cc_final: 0.6451 (mpt180) REVERT: A 27 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7698 (tp30) REVERT: A 35 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7265 (mm110) REVERT: A 296 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6510 (mp) REVERT: A 370 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6777 (mm-30) REVERT: B 9 GLN cc_start: 0.6442 (OUTLIER) cc_final: 0.6038 (mt0) REVERT: B 12 GLU cc_start: 0.6926 (tp30) cc_final: 0.6494 (tt0) REVERT: B 19 ARG cc_start: 0.7740 (ttp-110) cc_final: 0.7167 (ttm-80) REVERT: B 197 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.7729 (mmm160) REVERT: B 214 ARG cc_start: 0.7320 (mmt180) cc_final: 0.6883 (mmt180) REVERT: B 215 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: B 304 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7878 (ttp-170) REVERT: E 40 CYS cc_start: 0.2472 (OUTLIER) cc_final: 0.1900 (p) REVERT: G 13 ARG cc_start: 0.6242 (ttm170) cc_final: 0.5874 (ttm110) REVERT: R 48 MET cc_start: 0.4091 (ptp) cc_final: 0.3368 (ttt) REVERT: R 90 LEU cc_start: 0.2265 (OUTLIER) cc_final: 0.1456 (pt) REVERT: R 140 GLU cc_start: 0.6051 (mm-30) cc_final: 0.5629 (mp0) REVERT: R 171 VAL cc_start: 0.7251 (t) cc_final: 0.6886 (m) REVERT: R 254 THR cc_start: 0.6959 (m) cc_final: 0.6459 (p) REVERT: R 264 LEU cc_start: 0.7948 (tp) cc_final: 0.7663 (mt) REVERT: R 328 ARG cc_start: 0.7151 (mtt180) cc_final: 0.6683 (mtt-85) REVERT: R 343 LYS cc_start: 0.7992 (tttt) cc_final: 0.7369 (tmmt) REVERT: R 364 SER cc_start: 0.7982 (m) cc_final: 0.7219 (p) REVERT: R 367 MET cc_start: 0.5279 (tmm) cc_final: 0.5048 (tmm) REVERT: R 368 LEU cc_start: 0.6978 (mt) cc_final: 0.6681 (tp) outliers start: 23 outliers final: 12 residues processed: 185 average time/residue: 1.7235 time to fit residues: 339.1040 Evaluate side-chains 183 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 120 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 90 optimal weight: 0.0470 chunk 111 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 266 HIS N 13 GLN N 35 ASN R 257 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.196297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.132552 restraints weight = 9627.659| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.48 r_work: 0.3254 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10490 Z= 0.118 Angle : 0.586 19.072 14190 Z= 0.298 Chirality : 0.045 0.644 1558 Planarity : 0.004 0.041 1775 Dihedral : 8.394 76.937 1785 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.03 % Allowed : 16.26 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1251 helix: 2.31 (0.23), residues: 515 sheet: 0.05 (0.32), residues: 236 loop : -0.52 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 234 HIS 0.003 0.001 HIS A 41 PHE 0.012 0.001 PHE R 269 TYR 0.013 0.001 TYR R 56 ARG 0.008 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.01215 ( 2) link_NAG-ASN : angle 8.82947 ( 6) hydrogen bonds : bond 0.04340 ( 528) hydrogen bonds : angle 4.46913 ( 1489) SS BOND : bond 0.00368 ( 9) SS BOND : angle 0.94906 ( 18) covalent geometry : bond 0.00241 (10478) covalent geometry : angle 0.55710 (14166) Misc. bond : bond 0.00028 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14151.76 seconds wall clock time: 246 minutes 3.45 seconds (14763.45 seconds total)