Starting phenix.real_space_refine on Sat Aug 23 10:01:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f0k_28759/08_2025/8f0k_28759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f0k_28759/08_2025/8f0k_28759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f0k_28759/08_2025/8f0k_28759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f0k_28759/08_2025/8f0k_28759.map" model { file = "/net/cci-nas-00/data/ceres_data/8f0k_28759/08_2025/8f0k_28759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f0k_28759/08_2025/8f0k_28759.cif" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 78 5.16 5 C 6760 2.51 5 N 1761 2.21 5 O 1952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10553 Number of models: 1 Model: "" Number of chains: 13 Chain: "E" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "P" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 279 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} 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: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 3046 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 352} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1888 Classifications: {'peptide': 228} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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: "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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 358 Unusual residues: {'NAG': 3, 'P42': 1, 'PLM': 8, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.60, per 1000 atoms: 0.25 Number of scatterers: 10553 At special positions: 0 Unit cell: (99.125, 168.188, 93.4375, 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 78 16.00 P 2 15.00 O 1952 8.00 N 1761 7.00 C 6760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS E 82 " distance=2.04 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 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=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " 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 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 E 201 " - " ASN E 29 " " NAG E 202 " - " ASN E 71 " " NAG R 501 " - " ASN R 125 " " NAG R 502 " - " ASN R 130 " " NAG R 503 " - " ASN R 73 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 234.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2390 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 13 sheets defined 45.5% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'E' and resid 29 through 48 Proline residue: E 38 - end of helix Processing helix chain 'E' and resid 52 through 57 removed outlier: 4.249A pdb=" N CYS E 57 " --> pdb=" O TRP E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 80 removed outlier: 4.287A pdb=" N PHE E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 115 through 120 Processing helix chain 'E' and resid 120 through 141 Proline residue: E 126 - end of helix 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 removed outlier: 3.765A pdb=" N HIS P 18 " --> pdb=" O ASN P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 24 Processing helix chain 'R' and resid 42 through 62 Processing helix chain 'R' and resid 131 through 135 Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.539A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.565A pdb=" N ASN R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.944A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 268 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 removed outlier: 3.512A pdb=" N LYS R 340 " --> pdb=" O HIS R 336 " (cutoff:3.500A) 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 406 Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.537A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.624A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.893A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.653A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA3, first strand: chain 'R' and resid 90 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.434A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.973A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.560A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.800A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.276A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.583A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.507A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.748A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.172A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1488 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: 1.55 Time building geometry restraints manager: 1.04 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: 1724 1.32 - 1.45: 2933 1.45 - 1.57: 5975 1.57 - 1.70: 4 1.70 - 1.82: 112 Bond restraints: 10748 Sorted by residual: bond pdb=" N VAL R 250 " pdb=" CA VAL R 250 " ideal model delta sigma weight residual 1.461 1.498 -0.036 1.17e-02 7.31e+03 9.72e+00 bond pdb=" N THR R 254 " pdb=" CA THR R 254 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.19e-02 7.06e+03 8.34e+00 bond pdb=" N VAL E 79 " pdb=" CA VAL E 79 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.29e+00 bond pdb=" N GLU R 255 " pdb=" CA GLU R 255 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.15e-02 7.56e+03 8.25e+00 bond pdb=" N VAL R 249 " pdb=" CA VAL R 249 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.42e+00 ... (remaining 10743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 14214 1.93 - 3.86: 263 3.86 - 5.80: 30 5.80 - 7.73: 6 7.73 - 9.66: 1 Bond angle restraints: 14514 Sorted by residual: angle pdb=" N VAL R 250 " pdb=" CA VAL R 250 " pdb=" C VAL R 250 " ideal model delta sigma weight residual 110.42 116.66 -6.24 9.60e-01 1.09e+00 4.22e+01 angle pdb=" N PHE R 253 " pdb=" CA PHE R 253 " pdb=" C PHE R 253 " ideal model delta sigma weight residual 111.36 116.89 -5.53 1.09e+00 8.42e-01 2.58e+01 angle pdb=" C PHE R 172 " pdb=" CA PHE R 172 " pdb=" CB PHE R 172 " ideal model delta sigma weight residual 110.90 103.34 7.56 1.58e+00 4.01e-01 2.29e+01 angle pdb=" C ASN E 86 " pdb=" CA ASN E 86 " pdb=" CB ASN E 86 " ideal model delta sigma weight residual 108.87 115.57 -6.70 1.55e+00 4.16e-01 1.87e+01 angle pdb=" CA VAL R 171 " pdb=" C VAL R 171 " pdb=" O VAL R 171 " ideal model delta sigma weight residual 121.05 116.38 4.67 1.11e+00 8.12e-01 1.77e+01 ... (remaining 14509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.31: 6282 25.31 - 50.63: 261 50.63 - 75.94: 47 75.94 - 101.25: 11 101.25 - 126.57: 6 Dihedral angle restraints: 6607 sinusoidal: 2904 harmonic: 3703 Sorted by residual: dihedral pdb=" CB CYS R 72 " pdb=" SG CYS R 72 " pdb=" SG CYS R 112 " pdb=" CB CYS R 112 " ideal model delta sinusoidal sigma weight residual -86.00 -145.39 59.39 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 129.21 -36.21 1 1.00e+01 1.00e-02 1.85e+01 dihedral pdb=" N1 PTY R 514 " pdb=" C2 PTY R 514 " pdb=" C3 PTY R 514 " pdb=" O11 PTY R 514 " ideal model delta sinusoidal sigma weight residual 65.33 -61.24 126.57 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 6604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1341 0.053 - 0.106: 193 0.106 - 0.159: 46 0.159 - 0.212: 10 0.212 - 0.265: 4 Chirality restraints: 1594 Sorted by residual: chirality pdb=" C6 PTY R 514 " pdb=" C1 PTY R 514 " pdb=" C5 PTY R 514 " pdb=" O7 PTY R 514 " both_signs ideal model delta sigma weight residual False 2.49 2.22 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA ARG R 258 " pdb=" N ARG R 258 " pdb=" C ARG R 258 " pdb=" CB ARG R 258 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA PHE R 172 " pdb=" N PHE R 172 " pdb=" C PHE R 172 " pdb=" CB PHE R 172 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 1591 not shown) Planarity restraints: 1820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 202 " -0.328 2.00e-02 2.50e+03 2.76e-01 9.50e+02 pdb=" C7 NAG E 202 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG E 202 " -0.196 2.00e-02 2.50e+03 pdb=" N2 NAG E 202 " 0.474 2.00e-02 2.50e+03 pdb=" O7 NAG E 202 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 170 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C PHE R 170 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE R 170 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL R 171 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 175 " 0.011 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C SER R 175 " -0.041 2.00e-02 2.50e+03 pdb=" O SER R 175 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU R 176 " 0.014 2.00e-02 2.50e+03 ... (remaining 1817 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2322 2.78 - 3.31: 9812 3.31 - 3.84: 17739 3.84 - 4.37: 21830 4.37 - 4.90: 36870 Nonbonded interactions: 88573 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.252 3.040 nonbonded pdb=" CD GLU R 397 " pdb=" O HOH R 602 " model vdw 2.274 3.270 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.304 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR A 204 " pdb=" N SER A 205 " model vdw 2.319 3.120 ... (remaining 88568 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.930 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 23.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 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 0.104 10764 Z= 0.263 Angle : 0.603 10.348 14549 Z= 0.369 Chirality : 0.044 0.265 1594 Planarity : 0.007 0.276 1815 Dihedral : 14.281 126.565 4187 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.91 % Allowed : 9.83 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.21), residues: 1254 helix: -1.82 (0.16), residues: 509 sheet: -0.24 (0.32), residues: 232 loop : -0.54 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.019 0.001 TYR E 83 PHE 0.007 0.001 PHE B 199 TRP 0.007 0.001 TRP A 234 HIS 0.002 0.000 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00399 (10748) covalent geometry : angle 0.59430 (14514) SS BOND : bond 0.00199 ( 10) SS BOND : angle 0.92013 ( 20) hydrogen bonds : bond 0.23978 ( 528) hydrogen bonds : angle 8.14215 ( 1488) Misc. bond : bond 0.10365 ( 1) link_NAG-ASN : bond 0.00660 ( 5) link_NAG-ASN : angle 3.14742 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 211 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 131 VAL cc_start: 0.6974 (m) cc_final: 0.6758 (t) REVERT: E 133 MET cc_start: 0.5509 (mmm) cc_final: 0.5081 (mpm) REVERT: R 195 SER cc_start: 0.6745 (m) cc_final: 0.6316 (p) REVERT: R 225 PHE cc_start: 0.6191 (m-80) cc_final: 0.5886 (m-80) REVERT: R 314 PHE cc_start: 0.6289 (m-10) cc_final: 0.5874 (t80) REVERT: R 395 ASN cc_start: 0.6176 (t0) cc_final: 0.5832 (t0) REVERT: A 20 ARG cc_start: 0.6216 (mtm110) cc_final: 0.5755 (ttm110) REVERT: A 28 LYS cc_start: 0.7034 (ttpp) cc_final: 0.6807 (ttpp) REVERT: A 296 LEU cc_start: 0.6834 (mp) cc_final: 0.6507 (mt) REVERT: A 299 GLU cc_start: 0.5464 (mt-10) cc_final: 0.5250 (mt-10) REVERT: A 344 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7297 (mm-30) REVERT: B 45 MET cc_start: 0.7865 (mtt) cc_final: 0.7589 (mtm) REVERT: B 188 MET cc_start: 0.8426 (mmm) cc_final: 0.8151 (mmm) REVERT: G 21 MET cc_start: 0.5616 (mmm) cc_final: 0.5138 (mpm) REVERT: G 25 ILE cc_start: 0.6224 (pt) cc_final: 0.5892 (pt) REVERT: N 1 GLN cc_start: 0.6078 (tp-100) cc_final: 0.5826 (mm-40) REVERT: N 73 ASP cc_start: 0.7681 (t0) cc_final: 0.7410 (t0) outliers start: 10 outliers final: 2 residues processed: 218 average time/residue: 0.7550 time to fit residues: 173.7833 Evaluate side-chains 156 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain B residue 59 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.0170 chunk 113 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0570 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 ASN E 103 ASN P 22 ASN R 184 HIS R 201 HIS R 223 HIS R 399 GLN A 12 GLN A 14 ASN A 54 ASN A 59 GLN A 213 GLN A 267 GLN A 357 HIS A 387 HIS A 390 GLN B 9 GLN B 17 GLN B 175 GLN B 293 ASN N 84 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.237966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.214574 restraints weight = 7181.498| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 0.51 r_work: 0.4123 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.4068 rms_B_bonded: 1.43 restraints_weight: 0.2500 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10764 Z= 0.121 Angle : 0.551 10.897 14549 Z= 0.292 Chirality : 0.041 0.145 1594 Planarity : 0.004 0.043 1815 Dihedral : 10.186 124.241 1838 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.64 % Allowed : 11.92 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.23), residues: 1254 helix: 1.04 (0.21), residues: 520 sheet: -0.20 (0.32), residues: 228 loop : 0.04 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 197 TYR 0.011 0.001 TYR R 191 PHE 0.015 0.001 PHE N 29 TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00245 (10748) covalent geometry : angle 0.54841 (14514) SS BOND : bond 0.00224 ( 10) SS BOND : angle 0.79450 ( 20) hydrogen bonds : bond 0.05029 ( 528) hydrogen bonds : angle 4.98604 ( 1488) Misc. bond : bond 0.00000 ( 1) link_NAG-ASN : bond 0.00230 ( 5) link_NAG-ASN : angle 1.61300 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.265 Fit side-chains REVERT: R 169 ILE cc_start: 0.5882 (mt) cc_final: 0.5646 (mm) REVERT: R 174 ARG cc_start: 0.4552 (OUTLIER) cc_final: 0.3830 (mtm180) REVERT: R 195 SER cc_start: 0.6992 (m) cc_final: 0.6589 (p) REVERT: R 383 GLN cc_start: 0.6979 (tt0) cc_final: 0.6668 (tt0) REVERT: A 15 GLU cc_start: 0.5234 (OUTLIER) cc_final: 0.4977 (tt0) REVERT: A 296 LEU cc_start: 0.7326 (mp) cc_final: 0.7040 (mt) REVERT: A 310 ASP cc_start: 0.5605 (m-30) cc_final: 0.5324 (m-30) outliers start: 18 outliers final: 4 residues processed: 177 average time/residue: 0.6091 time to fit residues: 114.7461 Evaluate side-chains 159 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 16 optimal weight: 50.0000 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 17 optimal weight: 0.0170 chunk 78 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 overall best weight: 0.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 395 ASN A 213 GLN A 357 HIS B 88 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.236126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.214406 restraints weight = 7055.967| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 0.54 r_work: 0.4112 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.4057 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10764 Z= 0.127 Angle : 0.556 6.841 14549 Z= 0.296 Chirality : 0.042 0.149 1594 Planarity : 0.004 0.040 1815 Dihedral : 10.005 121.327 1837 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.73 % Allowed : 12.74 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.24), residues: 1254 helix: 1.87 (0.22), residues: 520 sheet: -0.00 (0.32), residues: 230 loop : 0.27 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 265 TYR 0.011 0.001 TYR A 339 PHE 0.014 0.002 PHE N 29 TRP 0.021 0.002 TRP A 234 HIS 0.007 0.001 HIS R 336 Details of bonding type rmsd covalent geometry : bond 0.00258 (10748) covalent geometry : angle 0.55455 (14514) SS BOND : bond 0.00445 ( 10) SS BOND : angle 0.85457 ( 20) hydrogen bonds : bond 0.04849 ( 528) hydrogen bonds : angle 4.85201 ( 1488) Misc. bond : bond 0.00021 ( 1) link_NAG-ASN : bond 0.00227 ( 5) link_NAG-ASN : angle 1.19763 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.297 Fit side-chains REVERT: E 48 MET cc_start: 0.1190 (OUTLIER) cc_final: 0.0723 (mtm) REVERT: R 169 ILE cc_start: 0.5800 (mt) cc_final: 0.5443 (mm) REVERT: R 174 ARG cc_start: 0.4563 (OUTLIER) cc_final: 0.3933 (mtm180) REVERT: R 195 SER cc_start: 0.7003 (m) cc_final: 0.6636 (p) REVERT: R 220 LYS cc_start: 0.5334 (mttt) cc_final: 0.5048 (mmtp) REVERT: R 257 GLN cc_start: 0.6907 (mt0) cc_final: 0.6682 (mt0) REVERT: R 383 GLN cc_start: 0.7065 (tt0) cc_final: 0.6746 (tt0) REVERT: A 16 GLU cc_start: 0.5075 (tp30) cc_final: 0.4531 (tp30) REVERT: A 296 LEU cc_start: 0.7375 (mp) cc_final: 0.7073 (mt) REVERT: A 310 ASP cc_start: 0.5862 (m-30) cc_final: 0.5521 (m-30) REVERT: B 217 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7084 (pmm) REVERT: N 106 ASP cc_start: 0.7550 (p0) cc_final: 0.7327 (p0) outliers start: 19 outliers final: 5 residues processed: 156 average time/residue: 0.7493 time to fit residues: 123.6724 Evaluate side-chains 149 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 69 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 119 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 186 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.233502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.211015 restraints weight = 7019.975| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 0.51 r_work: 0.4068 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.4009 rms_B_bonded: 1.45 restraints_weight: 0.2500 r_work: 0.3659 rms_B_bonded: 4.77 restraints_weight: 0.1250 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10764 Z= 0.187 Angle : 0.665 7.253 14549 Z= 0.353 Chirality : 0.045 0.159 1594 Planarity : 0.005 0.040 1815 Dihedral : 11.359 135.689 1837 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.18 % Allowed : 12.01 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.24), residues: 1254 helix: 1.76 (0.23), residues: 521 sheet: -0.03 (0.32), residues: 234 loop : 0.33 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 150 TYR 0.013 0.002 TYR A 339 PHE 0.019 0.002 PHE A 212 TRP 0.030 0.002 TRP A 234 HIS 0.015 0.002 HIS R 336 Details of bonding type rmsd covalent geometry : bond 0.00399 (10748) covalent geometry : angle 0.66315 (14514) SS BOND : bond 0.00494 ( 10) SS BOND : angle 0.90624 ( 20) hydrogen bonds : bond 0.05617 ( 528) hydrogen bonds : angle 5.14377 ( 1488) Misc. bond : bond 0.00051 ( 1) link_NAG-ASN : bond 0.00247 ( 5) link_NAG-ASN : angle 1.29103 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0860 (ptp) cc_final: 0.0590 (ppp) REVERT: R 48 MET cc_start: -0.0000 (mmt) cc_final: -0.0209 (tmt) REVERT: R 169 ILE cc_start: 0.6447 (mt) cc_final: 0.6163 (mm) REVERT: R 174 ARG cc_start: 0.4830 (OUTLIER) cc_final: 0.4253 (mtm180) REVERT: R 195 SER cc_start: 0.7439 (m) cc_final: 0.6971 (p) REVERT: R 257 GLN cc_start: 0.7221 (mt0) cc_final: 0.6917 (mt0) REVERT: R 383 GLN cc_start: 0.7360 (tt0) cc_final: 0.7007 (tt0) REVERT: R 408 GLN cc_start: 0.3045 (OUTLIER) cc_final: 0.2656 (tt0) REVERT: A 16 GLU cc_start: 0.5483 (tp30) cc_final: 0.4921 (tp30) REVERT: A 296 LEU cc_start: 0.7615 (mp) cc_final: 0.7315 (mt) REVERT: B 217 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7910 (pmm) REVERT: N 106 ASP cc_start: 0.7835 (p0) cc_final: 0.7455 (p0) outliers start: 24 outliers final: 12 residues processed: 157 average time/residue: 0.7083 time to fit residues: 117.8718 Evaluate side-chains 147 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 77 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 30.0000 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 31 ASN P 35 ASN R 396 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.233230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.208028 restraints weight = 6979.198| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 0.54 r_work: 0.4080 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.4025 rms_B_bonded: 1.43 restraints_weight: 0.2500 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10764 Z= 0.172 Angle : 0.637 7.477 14549 Z= 0.338 Chirality : 0.045 0.194 1594 Planarity : 0.004 0.037 1815 Dihedral : 11.484 133.758 1837 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.18 % Allowed : 12.37 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.24), residues: 1254 helix: 1.74 (0.23), residues: 521 sheet: 0.02 (0.33), residues: 229 loop : 0.32 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 265 TYR 0.014 0.002 TYR A 339 PHE 0.019 0.002 PHE A 212 TRP 0.030 0.002 TRP A 234 HIS 0.012 0.002 HIS R 336 Details of bonding type rmsd covalent geometry : bond 0.00366 (10748) covalent geometry : angle 0.63601 (14514) SS BOND : bond 0.00464 ( 10) SS BOND : angle 0.86542 ( 20) hydrogen bonds : bond 0.05304 ( 528) hydrogen bonds : angle 5.05408 ( 1488) Misc. bond : bond 0.00033 ( 1) link_NAG-ASN : bond 0.00265 ( 5) link_NAG-ASN : angle 1.13961 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: E 47 MET cc_start: 0.0669 (OUTLIER) cc_final: 0.0080 (mpp) REVERT: R 48 MET cc_start: 0.0250 (mmt) cc_final: -0.0372 (tmt) REVERT: R 169 ILE cc_start: 0.5956 (mt) cc_final: 0.5745 (mm) REVERT: R 174 ARG cc_start: 0.4564 (OUTLIER) cc_final: 0.3925 (mtm180) REVERT: R 195 SER cc_start: 0.7119 (m) cc_final: 0.6700 (p) REVERT: R 383 GLN cc_start: 0.7159 (tt0) cc_final: 0.6906 (tt0) REVERT: R 396 ASN cc_start: 0.4998 (t0) cc_final: 0.4750 (t0) REVERT: R 408 GLN cc_start: 0.2841 (OUTLIER) cc_final: 0.2359 (tt0) REVERT: A 16 GLU cc_start: 0.5213 (tp30) cc_final: 0.4686 (tp30) REVERT: A 296 LEU cc_start: 0.7418 (mp) cc_final: 0.7151 (mt) REVERT: A 299 GLU cc_start: 0.5323 (OUTLIER) cc_final: 0.5114 (tt0) REVERT: B 217 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7232 (pmm) REVERT: B 292 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8407 (m-10) REVERT: N 106 ASP cc_start: 0.7619 (p0) cc_final: 0.7400 (p0) outliers start: 24 outliers final: 10 residues processed: 156 average time/residue: 0.6985 time to fit residues: 115.4601 Evaluate side-chains 148 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 113 optimal weight: 0.4980 chunk 12 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 31 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.233908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.211088 restraints weight = 7096.646| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 0.53 r_work: 0.4096 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.4042 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10764 Z= 0.144 Angle : 0.595 8.783 14549 Z= 0.314 Chirality : 0.043 0.212 1594 Planarity : 0.004 0.036 1815 Dihedral : 11.115 119.650 1837 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.27 % Allowed : 12.19 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.24), residues: 1254 helix: 1.99 (0.23), residues: 517 sheet: 0.12 (0.33), residues: 226 loop : 0.32 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 317 TYR 0.011 0.001 TYR A 339 PHE 0.015 0.002 PHE A 212 TRP 0.026 0.002 TRP A 234 HIS 0.010 0.001 HIS R 336 Details of bonding type rmsd covalent geometry : bond 0.00304 (10748) covalent geometry : angle 0.59358 (14514) SS BOND : bond 0.00399 ( 10) SS BOND : angle 0.75607 ( 20) hydrogen bonds : bond 0.04896 ( 528) hydrogen bonds : angle 4.90523 ( 1488) Misc. bond : bond 0.00025 ( 1) link_NAG-ASN : bond 0.00184 ( 5) link_NAG-ASN : angle 1.18192 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: E 47 MET cc_start: 0.0325 (ptp) cc_final: -0.0088 (mpp) REVERT: R 48 MET cc_start: 0.0064 (mmt) cc_final: -0.0456 (tmt) REVERT: R 169 ILE cc_start: 0.5972 (mt) cc_final: 0.5712 (mm) REVERT: R 174 ARG cc_start: 0.4500 (OUTLIER) cc_final: 0.3813 (mtm180) REVERT: R 195 SER cc_start: 0.7025 (m) cc_final: 0.6628 (p) REVERT: R 383 GLN cc_start: 0.7150 (tt0) cc_final: 0.6907 (tt0) REVERT: R 408 GLN cc_start: 0.2904 (OUTLIER) cc_final: 0.2445 (tt0) REVERT: A 16 GLU cc_start: 0.5163 (tp30) cc_final: 0.4658 (tp30) REVERT: A 296 LEU cc_start: 0.7415 (mp) cc_final: 0.7158 (mt) REVERT: N 106 ASP cc_start: 0.7602 (p0) cc_final: 0.7401 (p0) outliers start: 25 outliers final: 12 residues processed: 156 average time/residue: 0.7088 time to fit residues: 117.2285 Evaluate side-chains 150 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 chunk 76 optimal weight: 0.3980 chunk 116 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN N 1 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.234170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.210090 restraints weight = 7059.104| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 0.54 r_work: 0.4100 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.4034 rms_B_bonded: 1.62 restraints_weight: 0.2500 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10764 Z= 0.135 Angle : 0.583 11.000 14549 Z= 0.306 Chirality : 0.042 0.212 1594 Planarity : 0.004 0.037 1815 Dihedral : 10.858 109.646 1837 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.00 % Allowed : 12.19 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.24), residues: 1254 helix: 2.03 (0.23), residues: 516 sheet: 0.11 (0.33), residues: 231 loop : 0.40 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 265 TYR 0.009 0.001 TYR N 117 PHE 0.015 0.002 PHE A 212 TRP 0.025 0.002 TRP A 234 HIS 0.011 0.001 HIS R 336 Details of bonding type rmsd covalent geometry : bond 0.00283 (10748) covalent geometry : angle 0.58186 (14514) SS BOND : bond 0.00360 ( 10) SS BOND : angle 0.68109 ( 20) hydrogen bonds : bond 0.04711 ( 528) hydrogen bonds : angle 4.85737 ( 1488) Misc. bond : bond 0.00021 ( 1) link_NAG-ASN : bond 0.00209 ( 5) link_NAG-ASN : angle 1.13766 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: E 47 MET cc_start: 0.0035 (ptp) cc_final: -0.0226 (mpt) REVERT: R 48 MET cc_start: 0.0087 (mmt) cc_final: -0.0324 (tmt) REVERT: R 169 ILE cc_start: 0.5995 (mt) cc_final: 0.5735 (mm) REVERT: R 174 ARG cc_start: 0.4515 (OUTLIER) cc_final: 0.3841 (mtm180) REVERT: R 195 SER cc_start: 0.7062 (m) cc_final: 0.6676 (p) REVERT: R 383 GLN cc_start: 0.7147 (tt0) cc_final: 0.6873 (tt0) REVERT: A 16 GLU cc_start: 0.5177 (tp30) cc_final: 0.4670 (tp30) REVERT: A 296 LEU cc_start: 0.7418 (mp) cc_final: 0.7156 (mt) REVERT: N 106 ASP cc_start: 0.7635 (p0) cc_final: 0.7402 (p0) outliers start: 22 outliers final: 12 residues processed: 149 average time/residue: 0.7643 time to fit residues: 122.3863 Evaluate side-chains 142 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.8980 chunk 82 optimal weight: 0.3980 chunk 4 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 97 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 336 HIS R 396 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.233417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.209641 restraints weight = 6946.374| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 0.54 r_work: 0.4085 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.4025 rms_B_bonded: 1.56 restraints_weight: 0.2500 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10764 Z= 0.155 Angle : 0.621 10.628 14549 Z= 0.326 Chirality : 0.044 0.239 1594 Planarity : 0.004 0.037 1815 Dihedral : 11.118 111.146 1837 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.91 % Allowed : 12.56 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.24), residues: 1254 helix: 1.89 (0.23), residues: 517 sheet: 0.02 (0.33), residues: 228 loop : 0.28 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 265 TYR 0.011 0.002 TYR R 299 PHE 0.016 0.002 PHE A 212 TRP 0.027 0.002 TRP A 234 HIS 0.004 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00327 (10748) covalent geometry : angle 0.62017 (14514) SS BOND : bond 0.00414 ( 10) SS BOND : angle 0.83351 ( 20) hydrogen bonds : bond 0.05054 ( 528) hydrogen bonds : angle 4.99893 ( 1488) Misc. bond : bond 0.00031 ( 1) link_NAG-ASN : bond 0.00234 ( 5) link_NAG-ASN : angle 1.16432 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: E 47 MET cc_start: -0.0049 (ptp) cc_final: -0.0284 (tpp) REVERT: R 48 MET cc_start: 0.0118 (mmt) cc_final: -0.0280 (mpt) REVERT: R 174 ARG cc_start: 0.4518 (OUTLIER) cc_final: 0.3833 (mtm180) REVERT: R 383 GLN cc_start: 0.7191 (tt0) cc_final: 0.6915 (tt0) REVERT: R 408 GLN cc_start: 0.2972 (OUTLIER) cc_final: 0.2533 (tt0) REVERT: A 16 GLU cc_start: 0.5243 (tp30) cc_final: 0.4732 (tp30) REVERT: A 296 LEU cc_start: 0.7420 (mp) cc_final: 0.7146 (mt) REVERT: N 106 ASP cc_start: 0.7626 (p0) cc_final: 0.7409 (p0) outliers start: 21 outliers final: 13 residues processed: 152 average time/residue: 0.8022 time to fit residues: 128.6825 Evaluate side-chains 148 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 92 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 396 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN N 1 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.233390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.210555 restraints weight = 6969.993| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 0.53 r_work: 0.4089 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.4034 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10764 Z= 0.155 Angle : 0.621 10.825 14549 Z= 0.325 Chirality : 0.044 0.227 1594 Planarity : 0.004 0.037 1815 Dihedral : 11.237 111.580 1837 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.91 % Allowed : 12.56 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.24), residues: 1254 helix: 1.91 (0.23), residues: 517 sheet: 0.05 (0.33), residues: 228 loop : 0.30 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 265 TYR 0.011 0.002 TYR R 299 PHE 0.016 0.002 PHE A 212 TRP 0.027 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00329 (10748) covalent geometry : angle 0.62020 (14514) SS BOND : bond 0.00428 ( 10) SS BOND : angle 0.80022 ( 20) hydrogen bonds : bond 0.04976 ( 528) hydrogen bonds : angle 4.96415 ( 1488) Misc. bond : bond 0.00025 ( 1) link_NAG-ASN : bond 0.00223 ( 5) link_NAG-ASN : angle 1.11267 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: E 47 MET cc_start: -0.0100 (ptp) cc_final: -0.0307 (tpp) REVERT: R 48 MET cc_start: 0.0169 (mmt) cc_final: -0.0237 (mpt) REVERT: R 174 ARG cc_start: 0.4519 (OUTLIER) cc_final: 0.3784 (mtm180) REVERT: R 338 TYR cc_start: 0.5339 (m-10) cc_final: 0.5006 (t80) REVERT: R 383 GLN cc_start: 0.7175 (tt0) cc_final: 0.6919 (tt0) REVERT: R 408 GLN cc_start: 0.2922 (OUTLIER) cc_final: 0.2516 (tt0) REVERT: A 16 GLU cc_start: 0.5190 (tp30) cc_final: 0.4656 (tp30) REVERT: A 296 LEU cc_start: 0.7410 (mp) cc_final: 0.7141 (mt) REVERT: N 106 ASP cc_start: 0.7607 (p0) cc_final: 0.7401 (p0) outliers start: 21 outliers final: 12 residues processed: 150 average time/residue: 0.8843 time to fit residues: 139.8992 Evaluate side-chains 145 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 86 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 396 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.234202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.211569 restraints weight = 6969.540| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 0.53 r_work: 0.4099 rms_B_bonded: 0.84 restraints_weight: 0.5000 r_work: 0.4052 rms_B_bonded: 1.30 restraints_weight: 0.2500 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10764 Z= 0.129 Angle : 0.579 11.597 14549 Z= 0.301 Chirality : 0.042 0.217 1594 Planarity : 0.004 0.037 1815 Dihedral : 10.707 102.149 1837 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.46 % Allowed : 13.10 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.24), residues: 1254 helix: 2.12 (0.23), residues: 512 sheet: 0.13 (0.33), residues: 231 loop : 0.39 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 11 TYR 0.009 0.001 TYR N 117 PHE 0.014 0.002 PHE A 212 TRP 0.025 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00269 (10748) covalent geometry : angle 0.57771 (14514) SS BOND : bond 0.00336 ( 10) SS BOND : angle 0.70637 ( 20) hydrogen bonds : bond 0.04523 ( 528) hydrogen bonds : angle 4.81623 ( 1488) Misc. bond : bond 0.00016 ( 1) link_NAG-ASN : bond 0.00177 ( 5) link_NAG-ASN : angle 1.02356 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: R 169 ILE cc_start: 0.5958 (mt) cc_final: 0.5706 (mm) REVERT: R 174 ARG cc_start: 0.4497 (OUTLIER) cc_final: 0.3731 (mtm180) REVERT: R 195 SER cc_start: 0.7027 (m) cc_final: 0.6648 (p) REVERT: R 338 TYR cc_start: 0.5341 (m-10) cc_final: 0.5018 (t80) REVERT: R 383 GLN cc_start: 0.7148 (tt0) cc_final: 0.6893 (tt0) REVERT: R 408 GLN cc_start: 0.2986 (OUTLIER) cc_final: 0.2554 (tt0) REVERT: A 16 GLU cc_start: 0.5134 (tp30) cc_final: 0.4601 (tp30) REVERT: A 296 LEU cc_start: 0.7401 (mp) cc_final: 0.7124 (mt) REVERT: N 106 ASP cc_start: 0.7589 (p0) cc_final: 0.7385 (p0) outliers start: 16 outliers final: 10 residues processed: 147 average time/residue: 0.8709 time to fit residues: 135.1484 Evaluate side-chains 143 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 292 SER Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 396 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.234668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.212627 restraints weight = 7060.796| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 0.53 r_work: 0.4107 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.4057 rms_B_bonded: 1.38 restraints_weight: 0.2500 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10764 Z= 0.122 Angle : 0.570 11.624 14549 Z= 0.295 Chirality : 0.042 0.207 1594 Planarity : 0.004 0.037 1815 Dihedral : 10.385 95.698 1837 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.36 % Allowed : 13.28 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.25), residues: 1254 helix: 2.18 (0.23), residues: 515 sheet: 0.16 (0.33), residues: 231 loop : 0.44 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 11 TYR 0.009 0.001 TYR N 80 PHE 0.015 0.001 PHE A 246 TRP 0.024 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00255 (10748) covalent geometry : angle 0.56882 (14514) SS BOND : bond 0.00302 ( 10) SS BOND : angle 0.66720 ( 20) hydrogen bonds : bond 0.04380 ( 528) hydrogen bonds : angle 4.76868 ( 1488) Misc. bond : bond 0.00019 ( 1) link_NAG-ASN : bond 0.00165 ( 5) link_NAG-ASN : angle 0.99821 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6104.53 seconds wall clock time: 104 minutes 21.84 seconds (6261.84 seconds total)