Starting phenix.real_space_refine on Tue Jul 29 12:23:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f0k_28759/07_2025/8f0k_28759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f0k_28759/07_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_28759/07_2025/8f0k_28759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f0k_28759/07_2025/8f0k_28759.map" model { file = "/net/cci-nas-00/data/ceres_data/8f0k_28759/07_2025/8f0k_28759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f0k_28759/07_2025/8f0k_28759.cif" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.70, per 1000 atoms: 0.73 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: 2.54 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.07 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: 3.29 Time building geometry restraints manager: 3.04 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: 2.350 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.680 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (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 TRP 0.007 0.001 TRP A 234 HIS 0.002 0.000 HIS R 381 PHE 0.007 0.001 PHE B 199 TYR 0.019 0.001 TYR E 83 ARG 0.004 0.000 ARG B 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00660 ( 5) link_NAG-ASN : angle 3.14742 ( 15) hydrogen bonds : bond 0.23978 ( 528) hydrogen bonds : angle 8.14215 ( 1488) SS BOND : bond 0.00199 ( 10) SS BOND : angle 0.92013 ( 20) covalent geometry : bond 0.00399 (10748) covalent geometry : angle 0.59430 (14514) Misc. bond : bond 0.10365 ( 1) *********************** 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 : 1.140 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: 0.5080 (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: 0.7296 (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: 1.5868 time to fit residues: 366.3210 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 : 1.145 ------------------------------------------------------------------------------- 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 103 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 58 optimal weight: 0.0870 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 overall best weight: 1.9562 ------------------------------------------------------------------------------- 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 357 HIS A 387 HIS A 390 GLN B 9 GLN B 17 GLN B 88 ASN 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 = 0.4483 r_free = 0.4483 target = 0.234528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.209803 restraints weight = 6935.534| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 0.51 r_work: 0.4071 rms_B_bonded: 0.85 restraints_weight: 0.5000 r_work: 0.4024 rms_B_bonded: 1.29 restraints_weight: 0.2500 r_work: 0.3701 rms_B_bonded: 4.51 restraints_weight: 0.1250 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10764 Z= 0.179 Angle : 0.657 11.936 14549 Z= 0.351 Chirality : 0.045 0.154 1594 Planarity : 0.005 0.044 1815 Dihedral : 11.123 132.444 1838 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.91 % Allowed : 11.01 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.23), residues: 1254 helix: 0.96 (0.21), residues: 520 sheet: -0.15 (0.32), residues: 237 loop : 0.18 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 234 HIS 0.008 0.002 HIS R 336 PHE 0.019 0.002 PHE N 29 TYR 0.015 0.002 TYR R 391 ARG 0.007 0.001 ARG B 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 5) link_NAG-ASN : angle 1.60904 ( 15) hydrogen bonds : bond 0.05971 ( 528) hydrogen bonds : angle 5.30212 ( 1488) SS BOND : bond 0.00363 ( 10) SS BOND : angle 0.93145 ( 20) covalent geometry : bond 0.00378 (10748) covalent geometry : angle 0.65496 (14514) Misc. bond : bond 0.00020 ( 1) *********************** 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 180 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 1.060 Fit side-chains REVERT: R 174 ARG cc_start: 0.4814 (OUTLIER) cc_final: 0.4199 (mtm180) REVERT: R 195 SER cc_start: 0.7348 (m) cc_final: 0.6928 (p) REVERT: R 383 GLN cc_start: 0.7328 (tt0) cc_final: 0.6969 (tt0) REVERT: A 265 ARG cc_start: 0.7505 (ptt-90) cc_final: 0.6959 (ppt90) REVERT: A 296 LEU cc_start: 0.7587 (mp) cc_final: 0.7289 (mt) REVERT: A 310 ASP cc_start: 0.6315 (m-30) cc_final: 0.5992 (m-30) REVERT: B 170 ASP cc_start: 0.8737 (t0) cc_final: 0.8465 (t70) REVERT: N 1 GLN cc_start: 0.6749 (tp-100) cc_final: 0.6485 (mm-40) REVERT: N 106 ASP cc_start: 0.7830 (p0) cc_final: 0.7429 (p0) outliers start: 21 outliers final: 5 residues processed: 173 average time/residue: 1.5075 time to fit residues: 277.1709 Evaluate side-chains 154 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 40 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 42 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 395 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 = 0.4493 r_free = 0.4493 target = 0.235525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.213541 restraints weight = 7158.531| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 0.54 r_work: 0.4109 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.4052 rms_B_bonded: 1.43 restraints_weight: 0.2500 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2598 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= 0.126 Angle : 0.552 6.560 14549 Z= 0.294 Chirality : 0.042 0.144 1594 Planarity : 0.004 0.043 1815 Dihedral : 10.426 120.108 1837 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.91 % Allowed : 12.19 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.24), residues: 1254 helix: 1.80 (0.22), residues: 521 sheet: 0.11 (0.32), residues: 228 loop : 0.28 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.003 0.001 HIS R 381 PHE 0.017 0.001 PHE E 44 TYR 0.011 0.001 TYR A 339 ARG 0.008 0.001 ARG B 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 5) link_NAG-ASN : angle 1.26389 ( 15) hydrogen bonds : bond 0.04822 ( 528) hydrogen bonds : angle 4.88574 ( 1488) SS BOND : bond 0.00288 ( 10) SS BOND : angle 0.81335 ( 20) covalent geometry : bond 0.00256 (10748) covalent geometry : angle 0.55075 (14514) Misc. bond : bond 0.00019 ( 1) *********************** 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 169 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.103 Fit side-chains REVERT: E 48 MET cc_start: 0.1141 (OUTLIER) cc_final: 0.0603 (mmm) REVERT: R 174 ARG cc_start: 0.4586 (OUTLIER) cc_final: 0.3925 (mtm180) REVERT: R 195 SER cc_start: 0.7018 (m) cc_final: 0.6655 (p) REVERT: R 383 GLN cc_start: 0.7052 (tt0) cc_final: 0.6731 (tt0) REVERT: A 265 ARG cc_start: 0.7203 (ptt-90) cc_final: 0.6680 (ppt90) REVERT: A 296 LEU cc_start: 0.7341 (mp) cc_final: 0.7062 (mt) REVERT: N 106 ASP cc_start: 0.7597 (p0) cc_final: 0.7375 (p0) outliers start: 21 outliers final: 5 residues processed: 159 average time/residue: 1.6113 time to fit residues: 272.0784 Evaluate side-chains 148 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 59 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 2 optimal weight: 0.0470 chunk 106 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.235379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.211667 restraints weight = 7032.141| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 0.53 r_work: 0.4092 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.4041 rms_B_bonded: 1.38 restraints_weight: 0.2500 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10764 Z= 0.126 Angle : 0.550 6.511 14549 Z= 0.293 Chirality : 0.042 0.150 1594 Planarity : 0.004 0.040 1815 Dihedral : 10.330 117.403 1837 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1254 helix: 2.03 (0.23), residues: 521 sheet: 0.03 (0.32), residues: 233 loop : 0.40 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.007 0.001 HIS R 336 PHE 0.015 0.001 PHE A 212 TYR 0.009 0.001 TYR A 339 ARG 0.005 0.001 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 5) link_NAG-ASN : angle 1.16896 ( 15) hydrogen bonds : bond 0.04633 ( 528) hydrogen bonds : angle 4.82956 ( 1488) SS BOND : bond 0.00332 ( 10) SS BOND : angle 0.77014 ( 20) covalent geometry : bond 0.00260 (10748) covalent geometry : angle 0.54850 (14514) Misc. bond : bond 0.00026 ( 1) *********************** 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: 17 poor density : 144 time to evaluate : 1.236 Fit side-chains REVERT: E 48 MET cc_start: 0.1095 (ptp) cc_final: 0.0844 (pp-130) REVERT: R 195 SER cc_start: 0.7027 (m) cc_final: 0.6666 (p) REVERT: R 220 LYS cc_start: 0.5354 (mttt) cc_final: 0.5081 (mmtp) REVERT: R 257 GLN cc_start: 0.7011 (mt0) cc_final: 0.6761 (mt0) REVERT: R 383 GLN cc_start: 0.7054 (tt0) cc_final: 0.6738 (tt0) REVERT: A 16 GLU cc_start: 0.5101 (tp30) cc_final: 0.4501 (tp30) REVERT: A 265 ARG cc_start: 0.7202 (ptt-90) cc_final: 0.6688 (ppt90) REVERT: A 296 LEU cc_start: 0.7398 (mp) cc_final: 0.7130 (mt) REVERT: B 217 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7179 (pmm) REVERT: N 106 ASP cc_start: 0.7594 (p0) cc_final: 0.7363 (p0) outliers start: 17 outliers final: 10 residues processed: 155 average time/residue: 1.6908 time to fit residues: 278.4831 Evaluate side-chains 150 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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 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 N residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 43 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 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 = 0.4494 r_free = 0.4494 target = 0.235649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.212100 restraints weight = 7032.096| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 0.53 r_work: 0.4102 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.4055 rms_B_bonded: 1.31 restraints_weight: 0.2500 r_work: 0.3697 rms_B_bonded: 4.93 restraints_weight: 0.1250 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10764 Z= 0.118 Angle : 0.535 7.888 14549 Z= 0.284 Chirality : 0.041 0.145 1594 Planarity : 0.003 0.039 1815 Dihedral : 9.940 116.036 1837 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1254 helix: 2.20 (0.23), residues: 521 sheet: 0.08 (0.33), residues: 226 loop : 0.47 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.004 0.001 HIS R 336 PHE 0.014 0.001 PHE A 212 TYR 0.009 0.001 TYR A 339 ARG 0.003 0.000 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 5) link_NAG-ASN : angle 1.05928 ( 15) hydrogen bonds : bond 0.04417 ( 528) hydrogen bonds : angle 4.72001 ( 1488) SS BOND : bond 0.00284 ( 10) SS BOND : angle 0.68135 ( 20) covalent geometry : bond 0.00241 (10748) covalent geometry : angle 0.53401 (14514) Misc. bond : bond 0.00019 ( 1) *********************** 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 166 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0558 (ptp) cc_final: 0.0043 (mpp) REVERT: R 174 ARG cc_start: 0.4787 (OUTLIER) cc_final: 0.4178 (mtm180) REVERT: R 195 SER cc_start: 0.7356 (m) cc_final: 0.6963 (p) REVERT: R 220 LYS cc_start: 0.5788 (mttt) cc_final: 0.5451 (mmtp) REVERT: R 257 GLN cc_start: 0.7179 (mt0) cc_final: 0.6897 (mt0) REVERT: R 383 GLN cc_start: 0.7282 (tt0) cc_final: 0.6946 (tt0) REVERT: R 408 GLN cc_start: 0.3075 (OUTLIER) cc_final: 0.2694 (tt0) REVERT: A 16 GLU cc_start: 0.5338 (tp30) cc_final: 0.4801 (tp30) REVERT: A 265 ARG cc_start: 0.7461 (ptt-90) cc_final: 0.6926 (ppt90) REVERT: A 296 LEU cc_start: 0.7607 (mp) cc_final: 0.7317 (mt) REVERT: B 217 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7902 (pmm) REVERT: N 73 ASP cc_start: 0.8570 (t0) cc_final: 0.8342 (t0) outliers start: 24 outliers final: 12 residues processed: 159 average time/residue: 1.5755 time to fit residues: 265.7049 Evaluate side-chains 150 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 336 HIS Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 15 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 B residue 217 MET Chi-restraints excluded: chain G residue 37 LEU 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 31 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 395 ASN R 396 ASN 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 = 0.4472 r_free = 0.4472 target = 0.233100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.209343 restraints weight = 7024.656| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 0.54 r_work: 0.4086 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.4035 rms_B_bonded: 1.34 restraints_weight: 0.2500 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10764 Z= 0.182 Angle : 0.655 7.819 14549 Z= 0.348 Chirality : 0.045 0.197 1594 Planarity : 0.005 0.044 1815 Dihedral : 11.035 130.107 1837 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.09 % Allowed : 12.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1254 helix: 1.98 (0.23), residues: 516 sheet: -0.11 (0.32), residues: 237 loop : 0.41 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 234 HIS 0.018 0.002 HIS R 336 PHE 0.018 0.002 PHE A 212 TYR 0.012 0.002 TYR R 299 ARG 0.005 0.001 ARG B 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 5) link_NAG-ASN : angle 1.20462 ( 15) hydrogen bonds : bond 0.05431 ( 528) hydrogen bonds : angle 5.05914 ( 1488) SS BOND : bond 0.00459 ( 10) SS BOND : angle 0.94237 ( 20) covalent geometry : bond 0.00385 (10748) covalent geometry : angle 0.65374 (14514) Misc. bond : bond 0.00046 ( 1) *********************** 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: 23 poor density : 140 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0528 (ptp) cc_final: 0.0051 (mpt) REVERT: R 48 MET cc_start: 0.0010 (mmt) cc_final: -0.0472 (tmt) REVERT: R 174 ARG cc_start: 0.4646 (OUTLIER) cc_final: 0.3956 (mtm180) REVERT: R 257 GLN cc_start: 0.7024 (mt0) cc_final: 0.6764 (mt0) REVERT: R 260 ARG cc_start: 0.5651 (ptp-170) cc_final: 0.5396 (ptp-170) REVERT: R 396 ASN cc_start: 0.4994 (t0) cc_final: 0.4759 (t0) REVERT: R 408 GLN cc_start: 0.2707 (OUTLIER) cc_final: 0.2224 (tt0) REVERT: A 16 GLU cc_start: 0.5220 (tp30) cc_final: 0.4689 (tp30) REVERT: A 265 ARG cc_start: 0.7203 (ptt-90) cc_final: 0.6962 (ttm-80) REVERT: A 296 LEU cc_start: 0.7416 (mp) cc_final: 0.7160 (mt) REVERT: B 217 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7237 (pmm) outliers start: 23 outliers final: 10 residues processed: 157 average time/residue: 1.8128 time to fit residues: 301.5115 Evaluate side-chains 149 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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 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 330 THR Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 37 LEU 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 35 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 114 optimal weight: 0.0670 chunk 21 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- 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 336 HIS R 395 ASN A 357 HIS A 390 GLN N 1 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.234023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.209289 restraints weight = 7059.578| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 0.55 r_work: 0.4086 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.4027 rms_B_bonded: 1.48 restraints_weight: 0.2500 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3291 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= 0.142 Angle : 0.586 9.112 14549 Z= 0.311 Chirality : 0.043 0.198 1594 Planarity : 0.004 0.038 1815 Dihedral : 10.617 115.386 1837 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.00 % Allowed : 12.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1254 helix: 2.06 (0.23), residues: 517 sheet: 0.10 (0.33), residues: 231 loop : 0.39 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 234 HIS 0.004 0.001 HIS R 302 PHE 0.016 0.002 PHE A 212 TYR 0.010 0.001 TYR N 117 ARG 0.004 0.001 ARG B 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 5) link_NAG-ASN : angle 1.14045 ( 15) hydrogen bonds : bond 0.04830 ( 528) hydrogen bonds : angle 4.88598 ( 1488) SS BOND : bond 0.00404 ( 10) SS BOND : angle 0.71202 ( 20) covalent geometry : bond 0.00298 (10748) covalent geometry : angle 0.58541 (14514) Misc. bond : bond 0.00026 ( 1) *********************** 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 158 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0241 (ptp) cc_final: -0.0017 (mpp) REVERT: R 48 MET cc_start: -0.0043 (mmt) cc_final: -0.0465 (tmt) REVERT: R 174 ARG cc_start: 0.4562 (OUTLIER) cc_final: 0.3865 (mtm180) REVERT: R 195 SER cc_start: 0.7076 (m) cc_final: 0.6678 (p) REVERT: R 257 GLN cc_start: 0.7031 (mt0) cc_final: 0.6770 (mt0) REVERT: R 383 GLN cc_start: 0.7087 (tt0) cc_final: 0.6763 (tt0) REVERT: R 408 GLN cc_start: 0.2936 (OUTLIER) cc_final: 0.2481 (tt0) REVERT: A 16 GLU cc_start: 0.5207 (tp30) cc_final: 0.4681 (tp30) REVERT: A 265 ARG cc_start: 0.7198 (ptt-90) cc_final: 0.6620 (ppt90) REVERT: A 296 LEU cc_start: 0.7408 (mp) cc_final: 0.7138 (mt) REVERT: B 217 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7289 (pmm) outliers start: 22 outliers final: 12 residues processed: 151 average time/residue: 1.9183 time to fit residues: 310.1293 Evaluate side-chains 150 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 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 347 ILE Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 37 LEU 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 99 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 105 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 396 ASN 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 = 0.233194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.209497 restraints weight = 6978.774| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 0.54 r_work: 0.4084 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.4028 rms_B_bonded: 1.44 restraints_weight: 0.2500 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10764 Z= 0.166 Angle : 0.633 9.702 14549 Z= 0.335 Chirality : 0.045 0.249 1594 Planarity : 0.005 0.061 1815 Dihedral : 11.064 115.106 1837 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.91 % Allowed : 12.92 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.24), residues: 1254 helix: 1.90 (0.23), residues: 517 sheet: -0.09 (0.33), residues: 237 loop : 0.36 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 234 HIS 0.005 0.001 HIS R 302 PHE 0.016 0.002 PHE A 212 TYR 0.012 0.002 TYR R 299 ARG 0.004 0.001 ARG B 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 5) link_NAG-ASN : angle 1.23035 ( 15) hydrogen bonds : bond 0.05242 ( 528) hydrogen bonds : angle 5.02611 ( 1488) SS BOND : bond 0.00458 ( 10) SS BOND : angle 0.93154 ( 20) covalent geometry : bond 0.00350 (10748) covalent geometry : angle 0.63129 (14514) Misc. bond : bond 0.00023 ( 1) *********************** 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 157 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0108 (ptp) cc_final: -0.0197 (tpp) REVERT: R 48 MET cc_start: -0.0004 (mmt) cc_final: -0.0447 (tmt) REVERT: R 174 ARG cc_start: 0.4602 (OUTLIER) cc_final: 0.3910 (mtm180) REVERT: R 338 TYR cc_start: 0.5352 (m-10) cc_final: 0.4977 (t80) REVERT: R 383 GLN cc_start: 0.7187 (tt0) cc_final: 0.6872 (tt0) REVERT: R 408 GLN cc_start: 0.2972 (OUTLIER) cc_final: 0.2514 (tt0) REVERT: A 16 GLU cc_start: 0.5220 (tp30) cc_final: 0.4699 (tp30) REVERT: A 265 ARG cc_start: 0.7220 (ptt-90) cc_final: 0.6973 (ttm-80) REVERT: A 296 LEU cc_start: 0.7421 (mp) cc_final: 0.7154 (mt) REVERT: B 217 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7336 (pmm) outliers start: 21 outliers final: 11 residues processed: 152 average time/residue: 1.6648 time to fit residues: 267.7436 Evaluate side-chains 146 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 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 B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 37 LEU 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 37 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 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 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 = 0.4487 r_free = 0.4487 target = 0.234745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.212234 restraints weight = 7080.695| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 0.56 r_work: 0.4117 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.4063 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10764 Z= 0.122 Angle : 0.562 11.246 14549 Z= 0.294 Chirality : 0.042 0.211 1594 Planarity : 0.004 0.059 1815 Dihedral : 10.662 103.616 1837 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.64 % Allowed : 13.38 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1254 helix: 2.16 (0.23), residues: 514 sheet: 0.04 (0.33), residues: 236 loop : 0.41 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.009 0.001 TYR N 117 ARG 0.007 0.000 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 5) link_NAG-ASN : angle 1.08313 ( 15) hydrogen bonds : bond 0.04437 ( 528) hydrogen bonds : angle 4.75306 ( 1488) SS BOND : bond 0.00305 ( 10) SS BOND : angle 0.65790 ( 20) covalent geometry : bond 0.00253 (10748) covalent geometry : angle 0.56131 (14514) Misc. bond : bond 0.00016 ( 1) *********************** 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 153 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0040 (ptp) cc_final: -0.0225 (tpp) REVERT: R 48 MET cc_start: -0.0039 (mmt) cc_final: -0.0402 (tmt) REVERT: R 174 ARG cc_start: 0.4522 (OUTLIER) cc_final: 0.3792 (mtm180) REVERT: R 195 SER cc_start: 0.7013 (m) cc_final: 0.6652 (p) REVERT: R 338 TYR cc_start: 0.5331 (m-10) cc_final: 0.5028 (t80) REVERT: R 383 GLN cc_start: 0.7057 (tt0) cc_final: 0.6754 (tt0) REVERT: R 408 GLN cc_start: 0.2998 (OUTLIER) cc_final: 0.2556 (tt0) REVERT: A 16 GLU cc_start: 0.5084 (tp30) cc_final: 0.4535 (tp30) REVERT: A 265 ARG cc_start: 0.7185 (ptt-90) cc_final: 0.6608 (ppt90) REVERT: A 296 LEU cc_start: 0.7390 (mp) cc_final: 0.7127 (mt) outliers start: 18 outliers final: 10 residues processed: 146 average time/residue: 1.6989 time to fit residues: 262.4070 Evaluate side-chains 148 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 347 ILE Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 37 LEU 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 35 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 84 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 53 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 396 ASN 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 = 0.4483 r_free = 0.4483 target = 0.234253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.210367 restraints weight = 7001.950| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 0.53 r_work: 0.4099 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.4051 rms_B_bonded: 1.32 restraints_weight: 0.2500 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10764 Z= 0.132 Angle : 0.583 12.731 14549 Z= 0.305 Chirality : 0.043 0.220 1594 Planarity : 0.004 0.057 1815 Dihedral : 10.684 102.339 1837 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.55 % Allowed : 13.92 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1254 helix: 2.08 (0.23), residues: 514 sheet: 0.13 (0.33), residues: 231 loop : 0.36 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.002 PHE A 212 TYR 0.009 0.001 TYR N 117 ARG 0.004 0.001 ARG P 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 5) link_NAG-ASN : angle 1.10060 ( 15) hydrogen bonds : bond 0.04615 ( 528) hydrogen bonds : angle 4.83642 ( 1488) SS BOND : bond 0.00330 ( 10) SS BOND : angle 0.69818 ( 20) covalent geometry : bond 0.00274 (10748) covalent geometry : angle 0.58200 (14514) Misc. bond : bond 0.00017 ( 1) ********************** 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 150 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: -0.0006 (ptp) cc_final: -0.0256 (tpp) REVERT: R 48 MET cc_start: -0.0086 (mmt) cc_final: -0.0443 (tmt) REVERT: R 141 LYS cc_start: 0.4791 (mmtp) cc_final: 0.4558 (mttp) REVERT: R 174 ARG cc_start: 0.4513 (OUTLIER) cc_final: 0.3797 (mtm180) REVERT: R 195 SER cc_start: 0.7006 (m) cc_final: 0.6638 (p) REVERT: R 338 TYR cc_start: 0.5317 (m-10) cc_final: 0.4991 (t80) REVERT: R 383 GLN cc_start: 0.7090 (tt0) cc_final: 0.6743 (tt0) REVERT: R 408 GLN cc_start: 0.2950 (OUTLIER) cc_final: 0.2516 (tt0) REVERT: A 16 GLU cc_start: 0.5109 (tp30) cc_final: 0.4598 (tp30) REVERT: A 265 ARG cc_start: 0.7193 (ptt-90) cc_final: 0.6613 (ppt90) REVERT: A 296 LEU cc_start: 0.7400 (mp) cc_final: 0.7142 (mt) outliers start: 17 outliers final: 10 residues processed: 145 average time/residue: 1.6956 time to fit residues: 260.0804 Evaluate side-chains 142 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 15 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 37 LEU 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 109 optimal weight: 0.0040 chunk 35 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 396 ASN 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 = 0.4487 r_free = 0.4487 target = 0.234736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.211103 restraints weight = 6996.979| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 0.54 r_work: 0.4108 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.4049 rms_B_bonded: 1.54 restraints_weight: 0.2500 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10764 Z= 0.123 Angle : 0.565 10.429 14549 Z= 0.295 Chirality : 0.042 0.211 1594 Planarity : 0.004 0.051 1815 Dihedral : 10.413 96.874 1837 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.36 % Allowed : 13.92 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.24), residues: 1254 helix: 2.12 (0.23), residues: 514 sheet: 0.13 (0.33), residues: 231 loop : 0.41 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.009 0.001 TYR N 117 ARG 0.006 0.000 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 5) link_NAG-ASN : angle 1.01007 ( 15) hydrogen bonds : bond 0.04411 ( 528) hydrogen bonds : angle 4.77159 ( 1488) SS BOND : bond 0.00305 ( 10) SS BOND : angle 0.69153 ( 20) covalent geometry : bond 0.00255 (10748) covalent geometry : angle 0.56457 (14514) Misc. bond : bond 0.00016 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17119.41 seconds wall clock time: 304 minutes 20.61 seconds (18260.61 seconds total)