Starting phenix.real_space_refine on Fri Jul 3 01:17:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f0k_28759/07_2026/8f0k_28759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f0k_28759/07_2026/8f0k_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 { model { file = "/net/cci-nas-00/data/ceres_data/8f0k_28759/07_2026/8f0k_28759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f0k_28759/07_2026/8f0k_28759.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f0k_28759/07_2026/8f0k_28759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f0k_28759/07_2026/8f0k_28759.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8f0k_28759/07_2026/8f0k_28759.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f0k_28759/07_2026/8f0k_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-dev-6108/lib/python3.11/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 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 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: 2.48, per 1000 atoms: 0.24 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: 0.73 Conformation dependent library (CDL) restraints added in 263.2 milliseconds 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: 0.17 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: 1.80 Time building geometry restraints manager: 0.99 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: 6067 25.31 - 50.63: 238 50.63 - 75.94: 42 75.94 - 101.25: 10 101.25 - 126.57: 6 Dihedral angle restraints: 6363 sinusoidal: 2660 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 6360 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: 2.900 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.270 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:9.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 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 : 14.208 126.565 3943 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 are 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/Z covalent geometry : bond 0.00399 / 0.24 (10748) covalent geometry : angle 0.59430 / 0.37 (14514) SS BOND : bond 0.00199 / 0.13 ( 10) SS BOND : angle 0.92013 / 0.66 ( 20) hydrogen bonds : bond 0.23978 / 15.63 ( 528) hydrogen bonds : angle 8.14215 / 5.82 ( 1488) Misc. bond : bond 0.10365 / 6.48 ( 1) link_NAG-ASN : bond 0.00660 / 0.38 ( 5) link_NAG-ASN : angle 3.14742 / 2.02 ( 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: 0.6315 (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: 0.6625 time to fit residues: 152.9451 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 : 0.256 ------------------------------------------------------------------------------- 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... 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 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.238044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.215368 restraints weight = 7184.028| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 0.52 r_work: 0.4124 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.4068 rms_B_bonded: 1.48 restraints_weight: 0.2500 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10764 Z= 0.124 Angle : 0.547 10.548 14549 Z= 0.290 Chirality : 0.041 0.160 1594 Planarity : 0.004 0.044 1815 Dihedral : 9.180 118.908 1594 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.55 % Allowed : 11.83 % Favored : 86.62 % 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 are not related in a simple way. whole: 0.51 (0.23), residues: 1254 helix: 1.04 (0.21), residues: 520 sheet: -0.10 (0.33), residues: 217 loop : -0.04 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 11 TYR 0.011 0.001 TYR A 339 PHE 0.015 0.001 PHE N 29 TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (10748) covalent geometry : angle 0.54346 / 0.29 (14514) SS BOND : bond 0.00207 / 0.14 ( 10) SS BOND : angle 0.78555 / 0.62 ( 20) hydrogen bonds : bond 0.05321 / 3.50 ( 528) hydrogen bonds : angle 5.02683 / 3.53 ( 1488) Misc. bond : bond 0.00070 / 0.04 ( 1) link_NAG-ASN : bond 0.00208 / 0.13 ( 5) link_NAG-ASN : angle 1.83086 / 1.06 ( 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 178 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.384 Fit side-chains REVERT: R 48 MET cc_start: 0.0082 (ttm) cc_final: -0.0322 (mpp) REVERT: R 169 ILE cc_start: 0.5890 (mt) cc_final: 0.5649 (mm) REVERT: R 174 ARG cc_start: 0.4572 (OUTLIER) cc_final: 0.3856 (mtm180) REVERT: R 195 SER cc_start: 0.7009 (m) cc_final: 0.6599 (p) REVERT: R 383 GLN cc_start: 0.6975 (tt0) cc_final: 0.6660 (tt0) REVERT: A 15 GLU cc_start: 0.5250 (OUTLIER) cc_final: 0.4985 (tt0) REVERT: A 296 LEU cc_start: 0.7336 (mp) cc_final: 0.7071 (mt) REVERT: A 310 ASP cc_start: 0.5579 (m-30) cc_final: 0.5307 (m-30) REVERT: N 106 ASP cc_start: 0.7441 (p0) cc_final: 0.7210 (p0) outliers start: 17 outliers final: 2 residues processed: 172 average time/residue: 0.6556 time to fit residues: 120.0073 Evaluate side-chains 156 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 B residue 59 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4496 r_free = 0.4496 target = 0.235997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.212921 restraints weight = 7031.176| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 0.52 r_work: 0.4099 rms_B_bonded: 0.84 restraints_weight: 0.5000 r_work: 0.4045 rms_B_bonded: 1.37 restraints_weight: 0.2500 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10764 Z= 0.131 Angle : 0.557 6.674 14549 Z= 0.297 Chirality : 0.042 0.150 1594 Planarity : 0.004 0.040 1815 Dihedral : 8.917 117.478 1593 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.46 % Allowed : 12.83 % Favored : 85.71 % 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 are not related in a simple way. whole: 1.27 (0.24), residues: 1254 helix: 1.89 (0.22), residues: 520 sheet: 0.02 (0.32), residues: 230 loop : 0.26 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 74 TYR 0.011 0.001 TYR N 95 PHE 0.018 0.002 PHE E 44 TRP 0.022 0.002 TRP A 234 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (10748) covalent geometry : angle 0.55582 / 0.30 (14514) SS BOND : bond 0.00241 / 0.15 ( 10) SS BOND : angle 0.71633 / 0.56 ( 20) hydrogen bonds : bond 0.04861 / 3.23 ( 528) hydrogen bonds : angle 4.88504 / 3.44 ( 1488) Misc. bond : bond 0.00023 / 0.01 ( 1) link_NAG-ASN : bond 0.00256 / 0.15 ( 5) link_NAG-ASN : angle 1.11503 / 0.65 ( 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 162 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.392 Fit side-chains REVERT: E 47 MET cc_start: 0.0563 (ttm) cc_final: 0.0356 (pmm) REVERT: E 48 MET cc_start: 0.0799 (OUTLIER) cc_final: 0.0459 (mmm) REVERT: R 169 ILE cc_start: 0.5812 (mt) cc_final: 0.5489 (mm) REVERT: R 174 ARG cc_start: 0.4574 (OUTLIER) cc_final: 0.3948 (mtm180) REVERT: R 195 SER cc_start: 0.7009 (m) cc_final: 0.6636 (p) REVERT: R 257 GLN cc_start: 0.6940 (mt0) cc_final: 0.6713 (mt0) REVERT: R 383 GLN cc_start: 0.7064 (tt0) cc_final: 0.6749 (tt0) REVERT: A 16 GLU cc_start: 0.5086 (tp30) cc_final: 0.4537 (tp30) REVERT: A 296 LEU cc_start: 0.7346 (mp) cc_final: 0.7049 (mt) REVERT: A 310 ASP cc_start: 0.5932 (m-30) cc_final: 0.5580 (m-30) outliers start: 16 outliers final: 6 residues processed: 155 average time/residue: 0.6819 time to fit residues: 111.9962 Evaluate side-chains 147 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 A residue 50 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 113 THR 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: 0.0670 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 119 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 186 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 = 0.4476 r_free = 0.4476 target = 0.233814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.210482 restraints weight = 7009.608| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 0.55 r_work: 0.4084 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.4029 rms_B_bonded: 1.47 restraints_weight: 0.2500 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3012 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= 0.175 Angle : 0.643 7.149 14549 Z= 0.342 Chirality : 0.045 0.157 1594 Planarity : 0.005 0.036 1815 Dihedral : 10.221 134.694 1593 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.09 % Allowed : 12.10 % 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 are not related in a simple way. whole: 1.23 (0.24), residues: 1254 helix: 1.84 (0.22), residues: 521 sheet: -0.07 (0.32), residues: 237 loop : 0.32 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 265 TYR 0.014 0.002 TYR A 339 PHE 0.017 0.002 PHE A 212 TRP 0.028 0.002 TRP A 234 HIS 0.005 0.002 HIS R 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (10748) covalent geometry : angle 0.64151 / 0.34 (14514) SS BOND : bond 0.00396 / 0.23 ( 10) SS BOND : angle 0.94503 / 0.56 ( 20) hydrogen bonds : bond 0.05435 / 3.62 ( 528) hydrogen bonds : angle 5.11167 / 3.60 ( 1488) Misc. bond : bond 0.00029 / 0.02 ( 1) link_NAG-ASN : bond 0.00208 / 0.14 ( 5) link_NAG-ASN : angle 1.18199 / 0.66 ( 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 164 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: E 48 MET cc_start: 0.0841 (OUTLIER) cc_final: 0.0470 (mmm) REVERT: R 169 ILE cc_start: 0.5951 (mt) cc_final: 0.5699 (mm) REVERT: R 174 ARG cc_start: 0.4603 (OUTLIER) cc_final: 0.3987 (mtm180) REVERT: R 195 SER cc_start: 0.7130 (m) cc_final: 0.6705 (p) REVERT: R 257 GLN cc_start: 0.7022 (mt0) cc_final: 0.6770 (mt0) REVERT: R 383 GLN cc_start: 0.7167 (tt0) cc_final: 0.6883 (tt0) REVERT: R 408 GLN cc_start: 0.2704 (OUTLIER) cc_final: 0.2198 (tt0) REVERT: A 16 GLU cc_start: 0.5178 (tp30) cc_final: 0.4643 (tp30) REVERT: A 296 LEU cc_start: 0.7419 (mp) cc_final: 0.7158 (mt) REVERT: B 217 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7235 (pmm) REVERT: N 106 ASP cc_start: 0.7605 (p0) cc_final: 0.7381 (p0) outliers start: 23 outliers final: 8 residues processed: 158 average time/residue: 0.6257 time to fit residues: 104.7065 Evaluate side-chains 151 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 48 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 408 GLN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 50 GLU 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: 3.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4481 r_free = 0.4481 target = 0.234153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.210138 restraints weight = 6996.536| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 0.54 r_work: 0.4095 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.4018 rms_B_bonded: 1.74 restraints_weight: 0.2500 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3133 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= 0.143 Angle : 0.581 7.462 14549 Z= 0.309 Chirality : 0.042 0.149 1594 Planarity : 0.004 0.038 1815 Dihedral : 9.984 129.926 1593 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.55 % Allowed : 12.83 % Favored : 85.62 % 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 are not related in a simple way. whole: 1.38 (0.24), residues: 1254 helix: 1.96 (0.23), residues: 521 sheet: 0.10 (0.33), residues: 230 loop : 0.33 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 265 TYR 0.012 0.001 TYR A 339 PHE 0.016 0.002 PHE A 212 TRP 0.026 0.002 TRP A 234 HIS 0.006 0.001 HIS R 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (10748) covalent geometry : angle 0.57957 / 0.31 (14514) SS BOND : bond 0.00352 / 0.21 ( 10) SS BOND : angle 0.76288 / 0.48 ( 20) hydrogen bonds : bond 0.04888 / 3.27 ( 528) hydrogen bonds : angle 4.91352 / 3.46 ( 1488) Misc. bond : bond 0.00024 / 0.01 ( 1) link_NAG-ASN : bond 0.00212 / 0.13 ( 5) link_NAG-ASN : angle 1.08169 / 0.63 ( 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 155 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: R 169 ILE cc_start: 0.6003 (mt) cc_final: 0.5744 (mm) REVERT: R 174 ARG cc_start: 0.4580 (OUTLIER) cc_final: 0.3933 (mtm180) REVERT: R 195 SER cc_start: 0.7063 (m) cc_final: 0.6678 (p) REVERT: R 257 GLN cc_start: 0.7019 (mt0) cc_final: 0.6770 (mt0) REVERT: R 383 GLN cc_start: 0.7157 (tt0) cc_final: 0.6906 (tt0) REVERT: A 296 LEU cc_start: 0.7427 (mp) cc_final: 0.7165 (mt) REVERT: B 217 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7339 (pmm) REVERT: B 292 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8320 (m-10) REVERT: N 106 ASP cc_start: 0.7634 (p0) cc_final: 0.7386 (p0) outliers start: 17 outliers final: 8 residues processed: 148 average time/residue: 0.6488 time to fit residues: 101.7098 Evaluate side-chains 142 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE 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: 9.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4468 r_free = 0.4468 target = 0.232848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.208485 restraints weight = 7078.897| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 0.54 r_work: 0.4071 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.4011 rms_B_bonded: 1.50 restraints_weight: 0.2500 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10764 Z= 0.173 Angle : 0.644 8.175 14549 Z= 0.341 Chirality : 0.045 0.194 1594 Planarity : 0.005 0.042 1815 Dihedral : 10.574 132.631 1593 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.91 % Allowed : 12.37 % Favored : 85.71 % 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 are not related in a simple way. whole: 1.24 (0.24), residues: 1254 helix: 1.87 (0.23), residues: 517 sheet: -0.06 (0.32), residues: 235 loop : 0.29 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 265 TYR 0.012 0.002 TYR A 339 PHE 0.016 0.002 PHE A 212 TRP 0.030 0.002 TRP A 234 HIS 0.006 0.001 HIS R 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (10748) covalent geometry : angle 0.64245 / 0.34 (14514) SS BOND : bond 0.00478 / 0.28 ( 10) SS BOND : angle 0.84788 / 0.54 ( 20) hydrogen bonds : bond 0.05356 / 3.58 ( 528) hydrogen bonds : angle 5.05925 / 3.57 ( 1488) Misc. bond : bond 0.00051 / 0.03 ( 1) link_NAG-ASN : bond 0.00178 / 0.11 ( 5) link_NAG-ASN : angle 1.21012 / 0.70 ( 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 155 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 48 MET cc_start: 0.0970 (ttm) cc_final: 0.0352 (mmm) REVERT: R 48 MET cc_start: -0.0032 (mmt) cc_final: -0.0413 (tmt) REVERT: R 174 ARG cc_start: 0.4537 (OUTLIER) cc_final: 0.3864 (mtm180) REVERT: R 195 SER cc_start: 0.7106 (m) cc_final: 0.6680 (p) REVERT: R 383 GLN cc_start: 0.7212 (tt0) cc_final: 0.6919 (tt0) REVERT: R 408 GLN cc_start: 0.2925 (OUTLIER) cc_final: 0.2436 (tt0) REVERT: A 16 GLU cc_start: 0.5231 (tp30) cc_final: 0.4709 (tp30) REVERT: A 296 LEU cc_start: 0.7423 (mp) cc_final: 0.7146 (mt) REVERT: B 217 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7320 (pmm) REVERT: N 106 ASP cc_start: 0.7602 (p0) cc_final: 0.7377 (p0) outliers start: 21 outliers final: 10 residues processed: 149 average time/residue: 0.7105 time to fit residues: 112.2090 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 : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 76 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 396 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN N 1 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 = 0.4472 r_free = 0.4472 target = 0.233260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.209133 restraints weight = 7055.179| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 0.55 r_work: 0.4087 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.4031 rms_B_bonded: 1.43 restraints_weight: 0.2500 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3448 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= 0.156 Angle : 0.609 9.285 14549 Z= 0.322 Chirality : 0.044 0.210 1594 Planarity : 0.004 0.036 1815 Dihedral : 10.584 128.505 1593 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.73 % Allowed : 12.28 % Favored : 85.99 % 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 are not related in a simple way. whole: 1.32 (0.24), residues: 1254 helix: 1.96 (0.23), residues: 517 sheet: 0.02 (0.33), residues: 231 loop : 0.28 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 317 TYR 0.013 0.002 TYR A 339 PHE 0.016 0.002 PHE A 212 TRP 0.028 0.002 TRP A 234 HIS 0.005 0.001 HIS R 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (10748) covalent geometry : angle 0.60790 / 0.32 (14514) SS BOND : bond 0.00419 / 0.25 ( 10) SS BOND : angle 0.82133 / 0.52 ( 20) hydrogen bonds : bond 0.05004 / 3.36 ( 528) hydrogen bonds : angle 4.94026 / 3.49 ( 1488) Misc. bond : bond 0.00031 / 0.02 ( 1) link_NAG-ASN : bond 0.00197 / 0.12 ( 5) link_NAG-ASN : angle 1.15508 / 0.67 ( 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 153 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 48 MET cc_start: 0.0897 (ttm) cc_final: 0.0249 (mmm) REVERT: R 48 MET cc_start: 0.0072 (mmt) cc_final: -0.0478 (tmt) REVERT: R 174 ARG cc_start: 0.4503 (OUTLIER) cc_final: 0.3816 (mtm180) REVERT: R 383 GLN cc_start: 0.7161 (tt0) cc_final: 0.6911 (tt0) REVERT: R 408 GLN cc_start: 0.2975 (OUTLIER) cc_final: 0.2539 (tt0) REVERT: A 16 GLU cc_start: 0.5188 (tp30) cc_final: 0.4673 (tp30) REVERT: A 296 LEU cc_start: 0.7420 (mp) cc_final: 0.7145 (mt) REVERT: B 217 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7264 (pmm) REVERT: N 106 ASP cc_start: 0.7622 (p0) cc_final: 0.7420 (p0) outliers start: 19 outliers final: 9 residues processed: 150 average time/residue: 0.6804 time to fit residues: 108.0424 Evaluate side-chains 141 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 330 THR 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 B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER 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: 0.9990 chunk 82 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 97 optimal weight: 2.9990 chunk 108 optimal weight: 0.0070 chunk 16 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.233300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.210716 restraints weight = 6981.270| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 0.55 r_work: 0.4090 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.4036 rms_B_bonded: 1.43 restraints_weight: 0.2500 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3524 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 : 0.619 10.297 14549 Z= 0.325 Chirality : 0.044 0.202 1594 Planarity : 0.004 0.036 1815 Dihedral : 10.642 129.423 1593 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.82 % Allowed : 12.65 % 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 are not related in a simple way. whole: 1.28 (0.24), residues: 1254 helix: 1.93 (0.23), residues: 517 sheet: -0.04 (0.33), residues: 233 loop : 0.27 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 265 TYR 0.010 0.002 TYR R 299 PHE 0.015 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/Z covalent geometry : bond 0.00328 / 0.16 (10748) covalent geometry : angle 0.61800 / 0.32 (14514) SS BOND : bond 0.00409 / 0.24 ( 10) SS BOND : angle 0.80068 / 0.50 ( 20) hydrogen bonds : bond 0.05045 / 3.37 ( 528) hydrogen bonds : angle 4.97896 / 3.51 ( 1488) Misc. bond : bond 0.00027 / 0.02 ( 1) link_NAG-ASN : bond 0.00231 / 0.15 ( 5) link_NAG-ASN : angle 1.20986 / 0.70 ( 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 150 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 48 MET cc_start: 0.0822 (ttm) cc_final: 0.0325 (mmm) REVERT: R 48 MET cc_start: -0.0046 (mmt) cc_final: -0.0480 (tmt) REVERT: R 174 ARG cc_start: 0.4499 (OUTLIER) cc_final: 0.3792 (mtm180) REVERT: R 383 GLN cc_start: 0.7177 (tt0) cc_final: 0.6921 (tt0) REVERT: R 408 GLN cc_start: 0.2911 (OUTLIER) cc_final: 0.2493 (tt0) REVERT: A 16 GLU cc_start: 0.5198 (tp30) cc_final: 0.4660 (tp30) REVERT: A 296 LEU cc_start: 0.7414 (mp) cc_final: 0.7139 (mt) REVERT: B 217 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7259 (pmm) REVERT: N 106 ASP cc_start: 0.7622 (p0) cc_final: 0.7419 (p0) outliers start: 20 outliers final: 9 residues processed: 145 average time/residue: 0.7348 time to fit residues: 113.0122 Evaluate side-chains 138 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 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 B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER 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: 4.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 396 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN N 1 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 = 0.4480 r_free = 0.4480 target = 0.234022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.211805 restraints weight = 7029.535| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 0.54 r_work: 0.4102 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.4056 rms_B_bonded: 1.31 restraints_weight: 0.2500 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3538 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= 0.133 Angle : 0.590 13.067 14549 Z= 0.307 Chirality : 0.042 0.186 1594 Planarity : 0.004 0.037 1815 Dihedral : 10.346 126.398 1593 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.36 % Allowed : 12.83 % 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 are not related in a simple way. whole: 1.40 (0.24), residues: 1254 helix: 2.02 (0.23), residues: 517 sheet: 0.10 (0.33), residues: 231 loop : 0.31 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 265 TYR 0.010 0.001 TYR N 80 PHE 0.016 0.002 PHE R 225 TRP 0.025 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (10748) covalent geometry : angle 0.58929 / 0.31 (14514) SS BOND : bond 0.00328 / 0.20 ( 10) SS BOND : angle 0.70845 / 0.44 ( 20) hydrogen bonds : bond 0.04636 / 3.10 ( 528) hydrogen bonds : angle 4.84668 / 3.42 ( 1488) Misc. bond : bond 0.00010 / 0.01 ( 1) link_NAG-ASN : bond 0.00195 / 0.12 ( 5) link_NAG-ASN : angle 1.12381 / 0.66 ( 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 146 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: E 48 MET cc_start: 0.0939 (ttm) cc_final: 0.0433 (mmm) REVERT: R 48 MET cc_start: -0.0025 (mmt) cc_final: -0.0428 (tmt) REVERT: R 169 ILE cc_start: 0.5835 (mt) cc_final: 0.5623 (mm) REVERT: R 174 ARG cc_start: 0.4509 (OUTLIER) cc_final: 0.3768 (mtm180) REVERT: R 383 GLN cc_start: 0.7125 (tt0) cc_final: 0.6854 (tt0) REVERT: R 408 GLN cc_start: 0.2945 (OUTLIER) cc_final: 0.2526 (tt0) REVERT: A 16 GLU cc_start: 0.5159 (tp30) cc_final: 0.4631 (tp30) REVERT: A 296 LEU cc_start: 0.7399 (mp) cc_final: 0.7134 (mt) REVERT: B 217 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7239 (pmm) REVERT: N 106 ASP cc_start: 0.7598 (p0) cc_final: 0.7393 (p0) outliers start: 15 outliers final: 6 residues processed: 142 average time/residue: 0.7572 time to fit residues: 113.7869 Evaluate side-chains 136 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 330 THR Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET 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: 2.9990 chunk 106 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 396 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN B 266 HIS B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.233103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.209553 restraints weight = 6953.073| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 0.54 r_work: 0.4088 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.4032 rms_B_bonded: 1.35 restraints_weight: 0.2500 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10764 Z= 0.164 Angle : 0.645 11.224 14549 Z= 0.337 Chirality : 0.044 0.202 1594 Planarity : 0.004 0.036 1815 Dihedral : 10.696 131.668 1593 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.36 % Allowed : 13.19 % 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 are not related in a simple way. whole: 1.26 (0.24), residues: 1254 helix: 1.90 (0.23), residues: 516 sheet: -0.07 (0.33), residues: 234 loop : 0.30 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 265 TYR 0.012 0.002 TYR R 299 PHE 0.016 0.002 PHE A 212 TRP 0.028 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (10748) covalent geometry : angle 0.64341 / 0.34 (14514) SS BOND : bond 0.00424 / 0.25 ( 10) SS BOND : angle 0.86991 / 0.53 ( 20) hydrogen bonds : bond 0.05157 / 3.45 ( 528) hydrogen bonds : angle 5.03403 / 3.55 ( 1488) Misc. bond : bond 0.00021 / 0.01 ( 1) link_NAG-ASN : bond 0.00195 / 0.12 ( 5) link_NAG-ASN : angle 1.20279 / 0.69 ( 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 145 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: E 48 MET cc_start: 0.0909 (ttm) cc_final: 0.0468 (mmm) REVERT: R 48 MET cc_start: -0.0036 (mmt) cc_final: -0.0448 (tmt) REVERT: R 174 ARG cc_start: 0.4503 (OUTLIER) cc_final: 0.3770 (mtm180) REVERT: R 338 TYR cc_start: 0.5285 (m-10) cc_final: 0.4968 (t80) REVERT: R 383 GLN cc_start: 0.7220 (tt0) cc_final: 0.6927 (tt0) REVERT: R 408 GLN cc_start: 0.2985 (OUTLIER) cc_final: 0.2548 (tt0) REVERT: A 16 GLU cc_start: 0.5217 (tp30) cc_final: 0.4686 (tp30) REVERT: A 296 LEU cc_start: 0.7415 (mp) cc_final: 0.7136 (mt) REVERT: B 217 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7301 (pmm) outliers start: 15 outliers final: 8 residues processed: 141 average time/residue: 0.7832 time to fit residues: 116.6404 Evaluate side-chains 139 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 151 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE 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 B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET 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: 0.0370 chunk 72 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 396 ASN A 213 GLN A 357 HIS A 390 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.234892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.213133 restraints weight = 7117.591| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 0.53 r_work: 0.4114 rms_B_bonded: 0.85 restraints_weight: 0.5000 r_work: 0.4064 rms_B_bonded: 1.35 restraints_weight: 0.2500 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10764 Z= 0.117 Angle : 0.563 11.767 14549 Z= 0.291 Chirality : 0.041 0.178 1594 Planarity : 0.004 0.037 1815 Dihedral : 9.929 121.680 1593 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.09 % Allowed : 13.38 % 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 are not related in a simple way. whole: 1.53 (0.24), residues: 1254 helix: 2.19 (0.23), residues: 516 sheet: 0.03 (0.33), residues: 230 loop : 0.40 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 265 TYR 0.009 0.001 TYR N 117 PHE 0.014 0.001 PHE A 212 TRP 0.022 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (10748) covalent geometry : angle 0.56196 / 0.29 (14514) SS BOND : bond 0.00273 / 0.17 ( 10) SS BOND : angle 0.67672 / 0.42 ( 20) hydrogen bonds : bond 0.04283 / 2.86 ( 528) hydrogen bonds : angle 4.72246 / 3.32 ( 1488) Misc. bond : bond 0.00006 / 0.00 ( 1) link_NAG-ASN : bond 0.00177 / 0.11 ( 5) link_NAG-ASN : angle 1.06097 / 0.63 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5778.99 seconds wall clock time: 98 minutes 52.66 seconds (5932.66 seconds total)