Starting phenix.real_space_refine on Thu May 1 00:26:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oe4_16824/05_2025/8oe4_16824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oe4_16824/05_2025/8oe4_16824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oe4_16824/05_2025/8oe4_16824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oe4_16824/05_2025/8oe4_16824.map" model { file = "/net/cci-nas-00/data/ceres_data/8oe4_16824/05_2025/8oe4_16824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oe4_16824/05_2025/8oe4_16824.cif" } resolution = 3.6 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= 0.011 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 6273 2.51 5 N 1682 2.21 5 O 1934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9951 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2388 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 287} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1116 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 134} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2384 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 280} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3957 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 470} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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: "C" 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 Time building chain proxies: 6.36, per 1000 atoms: 0.64 Number of scatterers: 9951 At special positions: 0 Unit cell: (104.039, 135.447, 162.929, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1934 8.00 N 1682 7.00 C 6273 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 170 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS B 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 115 " distance=2.04 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 101 " distance=2.02 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 105 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 80 " - pdb=" SG CYS D 86 " distance=2.03 Simple disulfide: pdb=" SG CYS D 186 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 230 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 368 " distance=2.04 Simple disulfide: pdb=" SG CYS D 293 " - pdb=" SG CYS D 383 " distance=2.04 Simple disulfide: pdb=" SG CYS D 413 " - pdb=" SG CYS D 474 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 601 " - " ASN C 81 " " NAG C 602 " - " ASN C 141 " " NAG E 1 " - " ASN A 222 " " NAG F 1 " - " ASN C 180 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.2 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 28 sheets defined 11.0% alpha, 44.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'B' and resid 29 through 48 removed outlier: 3.735A pdb=" N HIS B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 85 Processing helix chain 'B' and resid 85 through 105 removed outlier: 4.560A pdb=" N CYS B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 92 " --> pdb=" O PHE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 119 through 136 removed outlier: 3.888A pdb=" N GLN B 123 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 187 removed outlier: 4.439A pdb=" N LEU B 160 " --> pdb=" O TRP B 156 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 186 No H-bonds generated for 'chain 'C' and resid 184 through 186' Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 426 through 430 removed outlier: 3.583A pdb=" N TRP D 430 " --> pdb=" O LEU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 447 Processing helix chain 'D' and resid 469 through 474 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 7.101A pdb=" N VAL A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 31 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N HIS A 105 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 33 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LYS A 107 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 35 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N CYS A 90 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N HIS A 99 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR A 88 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 27 removed outlier: 7.101A pdb=" N VAL A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 31 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N HIS A 105 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 33 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LYS A 107 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 35 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 49 Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 removed outlier: 4.753A pdb=" N LEU A 145 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 132 removed outlier: 3.634A pdb=" N ASN A 184 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER A 190 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU A 175 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 160 Processing sheet with id=AA8, first strand: chain 'A' and resid 239 through 245 removed outlier: 5.558A pdb=" N ASN A 240 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU A 257 " --> pdb=" O ASN A 240 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 244 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 253 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 279 removed outlier: 3.758A pdb=" N CYS A 274 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 308 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 32 through 37 removed outlier: 3.747A pdb=" N HIS C 33 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 43 removed outlier: 6.461A pdb=" N PHE C 42 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N CYS C 101 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY C 116 " --> pdb=" O MET C 99 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N MET C 99 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASP C 118 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA C 97 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR C 100 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS C 63 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 179 through 182 removed outlier: 4.014A pdb=" N ILE C 179 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN C 141 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE C 219 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C 135 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 175 Processing sheet with id=AB5, first strand: chain 'C' and resid 170 through 175 Processing sheet with id=AB6, first strand: chain 'C' and resid 223 through 231 removed outlier: 5.265A pdb=" N ILE C 225 " --> pdb=" O ASP C 243 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP C 243 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 280 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP C 242 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN C 278 " --> pdb=" O TRP C 242 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 266 through 272 removed outlier: 3.592A pdb=" N LYS C 268 " --> pdb=" O MET C 255 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET C 255 " --> pdb=" O LYS C 268 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 251 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 47 through 54 removed outlier: 4.296A pdb=" N LEU D 50 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER D 63 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N CYS D 52 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU D 61 " --> pdb=" O CYS D 52 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG D 54 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ARG D 59 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 86 through 92 removed outlier: 5.117A pdb=" N TYR D 88 " --> pdb=" O CYS D 79 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N CYS D 79 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ALA D 90 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU D 77 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY D 92 " --> pdb=" O HIS D 75 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 86 through 92 removed outlier: 5.117A pdb=" N TYR D 88 " --> pdb=" O CYS D 79 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N CYS D 79 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ALA D 90 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU D 77 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY D 92 " --> pdb=" O HIS D 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 146 through 151 Processing sheet with id=AC3, first strand: chain 'D' and resid 182 through 189 removed outlier: 3.655A pdb=" N CYS D 186 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL D 170 " --> pdb=" O CYS D 186 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA D 168 " --> pdb=" O PRO D 188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 242 through 245 removed outlier: 6.200A pdb=" N ARG D 242 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 298 through 302 Processing sheet with id=AC6, first strand: chain 'D' and resid 298 through 302 Processing sheet with id=AC7, first strand: chain 'D' and resid 346 through 349 Processing sheet with id=AC8, first strand: chain 'D' and resid 382 through 389 removed outlier: 4.217A pdb=" N TYR D 367 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N MET D 365 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS D 412 " --> pdb=" O GLY D 440 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ALA D 420 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N THR D 432 " --> pdb=" O ALA D 420 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 450 through 458 removed outlier: 5.874A pdb=" N HIS D 451 " --> pdb=" O ALA D 467 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA D 467 " --> pdb=" O HIS D 451 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER D 461 " --> pdb=" O HIS D 457 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 493 through 498 399 hydrogen bonds defined for protein. 1062 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: 3.61 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3202 1.34 - 1.47: 2530 1.47 - 1.59: 4394 1.59 - 1.71: 1 1.71 - 1.83: 78 Bond restraints: 10205 Sorted by residual: bond pdb=" CG PRO A 326 " pdb=" CD PRO A 326 " ideal model delta sigma weight residual 1.503 1.311 0.192 3.40e-02 8.65e+02 3.21e+01 bond pdb=" CB PRO A 326 " pdb=" CG PRO A 326 " ideal model delta sigma weight residual 1.492 1.671 -0.179 5.00e-02 4.00e+02 1.29e+01 bond pdb=" N PRO A 326 " pdb=" CD PRO A 326 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.23e+01 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.38e+00 bond pdb=" N PRO A 326 " pdb=" CA PRO A 326 " ideal model delta sigma weight residual 1.465 1.447 0.018 1.11e-02 8.12e+03 2.62e+00 ... (remaining 10200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 13767 3.31 - 6.62: 112 6.62 - 9.94: 10 9.94 - 13.25: 1 13.25 - 16.56: 2 Bond angle restraints: 13892 Sorted by residual: angle pdb=" CA PRO A 326 " pdb=" N PRO A 326 " pdb=" CD PRO A 326 " ideal model delta sigma weight residual 112.00 95.44 16.56 1.40e+00 5.10e-01 1.40e+02 angle pdb=" N PRO A 326 " pdb=" CD PRO A 326 " pdb=" CG PRO A 326 " ideal model delta sigma weight residual 103.20 91.36 11.84 1.50e+00 4.44e-01 6.23e+01 angle pdb=" CA PRO A 326 " pdb=" CB PRO A 326 " pdb=" CG PRO A 326 " ideal model delta sigma weight residual 104.50 95.89 8.61 1.90e+00 2.77e-01 2.06e+01 angle pdb=" N PRO A 326 " pdb=" CA PRO A 326 " pdb=" C PRO A 326 " ideal model delta sigma weight residual 112.01 120.10 -8.09 1.84e+00 2.95e-01 1.93e+01 angle pdb=" C ASN C 81 " pdb=" CA ASN C 81 " pdb=" CB ASN C 81 " ideal model delta sigma weight residual 110.43 116.93 -6.50 1.68e+00 3.54e-01 1.50e+01 ... (remaining 13887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.28: 5789 21.28 - 42.55: 385 42.55 - 63.83: 49 63.83 - 85.10: 15 85.10 - 106.38: 9 Dihedral angle restraints: 6247 sinusoidal: 2605 harmonic: 3642 Sorted by residual: dihedral pdb=" CB CYS D 24 " pdb=" SG CYS D 24 " pdb=" SG CYS D 30 " pdb=" CB CYS D 30 " ideal model delta sinusoidal sigma weight residual 93.00 153.18 -60.18 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CA ASN C 141 " pdb=" C ASN C 141 " pdb=" N MET C 142 " pdb=" CA MET C 142 " ideal model delta harmonic sigma weight residual 180.00 152.52 27.48 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CB CYS C 59 " pdb=" SG CYS C 59 " pdb=" SG CYS C 105 " pdb=" CB CYS C 105 " ideal model delta sinusoidal sigma weight residual -86.00 -129.31 43.31 1 1.00e+01 1.00e-02 2.61e+01 ... (remaining 6244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1261 0.062 - 0.124: 253 0.124 - 0.186: 22 0.186 - 0.248: 5 0.248 - 0.310: 1 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA PRO A 326 " pdb=" N PRO A 326 " pdb=" C PRO A 326 " pdb=" CB PRO A 326 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 222 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1539 not shown) Planarity restraints: 1781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 81 " 0.033 2.00e-02 2.50e+03 3.11e-02 1.21e+01 pdb=" CG ASN C 81 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN C 81 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 81 " -0.026 2.00e-02 2.50e+03 pdb=" C1 NAG C 601 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 325 " -0.056 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO A 326 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 222 " -0.027 2.00e-02 2.50e+03 2.53e-02 7.98e+00 pdb=" CG ASN A 222 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 222 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 222 " 0.024 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.025 2.00e-02 2.50e+03 ... (remaining 1778 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 664 2.74 - 3.28: 8931 3.28 - 3.82: 15796 3.82 - 4.36: 18796 4.36 - 4.90: 32359 Nonbonded interactions: 76546 Sorted by model distance: nonbonded pdb=" OD1 ASN A 135 " pdb=" OG SER A 137 " model vdw 2.196 3.040 nonbonded pdb=" O ASP A 84 " pdb=" OH TYR A 88 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR B 100 " pdb=" OG SER B 168 " model vdw 2.254 3.040 nonbonded pdb=" OG SER A 158 " pdb=" O GLU A 209 " model vdw 2.281 3.040 nonbonded pdb=" OE2 GLU B 101 " pdb=" OG SER B 132 " model vdw 2.285 3.040 ... (remaining 76541 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 9.240 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.550 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 : 0.005 0.192 10233 Z= 0.239 Angle : 0.863 16.562 13956 Z= 0.471 Chirality : 0.049 0.310 1542 Planarity : 0.006 0.098 1777 Dihedral : 14.527 106.377 3835 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.73 % Allowed : 12.74 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.38 (0.23), residues: 1231 helix: -0.14 (0.49), residues: 99 sheet: 0.21 (0.22), residues: 520 loop : -0.61 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 466 HIS 0.018 0.001 HIS D 438 PHE 0.026 0.002 PHE D 208 TYR 0.035 0.003 TYR D 357 ARG 0.022 0.001 ARG D 536 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 4) link_NAG-ASN : angle 4.70232 ( 12) link_BETA1-4 : bond 0.00605 ( 3) link_BETA1-4 : angle 2.04791 ( 9) link_ALPHA1-3 : bond 0.00275 ( 1) link_ALPHA1-3 : angle 1.94039 ( 3) hydrogen bonds : bond 0.23150 ( 353) hydrogen bonds : angle 8.59682 ( 1062) SS BOND : bond 0.00368 ( 20) SS BOND : angle 1.47407 ( 40) covalent geometry : bond 0.00540 (10205) covalent geometry : angle 0.84765 (13892) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8972 (tpp) cc_final: 0.8174 (tpp) REVERT: B 107 ASP cc_start: 0.9073 (p0) cc_final: 0.8549 (t0) REVERT: C 99 MET cc_start: 0.8464 (mmm) cc_final: 0.7499 (mmt) REVERT: C 184 ASP cc_start: 0.9244 (m-30) cc_final: 0.8527 (t0) REVERT: D 136 SER cc_start: 0.8247 (m) cc_final: 0.7954 (t) REVERT: D 143 LEU cc_start: 0.8429 (mt) cc_final: 0.8061 (pp) REVERT: D 408 MET cc_start: 0.6375 (mtt) cc_final: 0.2816 (tmm) outliers start: 8 outliers final: 3 residues processed: 121 average time/residue: 0.2698 time to fit residues: 44.6186 Evaluate side-chains 63 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain D residue 474 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 20.0000 chunk 93 optimal weight: 0.0060 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS D 121 ASN D 247 GLN D 339 HIS D 438 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.104678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.071365 restraints weight = 47368.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.070858 restraints weight = 27477.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.071137 restraints weight = 17773.186| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 10233 Z= 0.131 Angle : 0.653 9.941 13956 Z= 0.329 Chirality : 0.045 0.159 1542 Planarity : 0.004 0.060 1777 Dihedral : 7.385 70.178 1513 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.74 % Allowed : 15.86 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.14 (0.23), residues: 1231 helix: 0.66 (0.51), residues: 105 sheet: 0.35 (0.21), residues: 514 loop : -0.55 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 371 HIS 0.007 0.001 HIS D 438 PHE 0.025 0.001 PHE C 75 TYR 0.017 0.002 TYR C 136 ARG 0.006 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 4) link_NAG-ASN : angle 3.04201 ( 12) link_BETA1-4 : bond 0.00342 ( 3) link_BETA1-4 : angle 1.96398 ( 9) link_ALPHA1-3 : bond 0.00762 ( 1) link_ALPHA1-3 : angle 2.08321 ( 3) hydrogen bonds : bond 0.04768 ( 353) hydrogen bonds : angle 6.21624 ( 1062) SS BOND : bond 0.00267 ( 20) SS BOND : angle 1.45080 ( 40) covalent geometry : bond 0.00300 (10205) covalent geometry : angle 0.64123 (13892) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8395 (tpp) cc_final: 0.8144 (tpp) REVERT: A 270 SER cc_start: 0.9249 (m) cc_final: 0.8835 (p) REVERT: B 39 LYS cc_start: 0.8603 (tttp) cc_final: 0.8292 (mtmm) REVERT: B 107 ASP cc_start: 0.8930 (p0) cc_final: 0.8519 (t0) REVERT: C 75 PHE cc_start: 0.7890 (t80) cc_final: 0.7689 (t80) REVERT: C 99 MET cc_start: 0.8778 (mmm) cc_final: 0.7862 (mmt) REVERT: C 126 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8578 (p0) REVERT: C 184 ASP cc_start: 0.9300 (m-30) cc_final: 0.8774 (t0) REVERT: D 136 SER cc_start: 0.8592 (m) cc_final: 0.8162 (t) REVERT: D 143 LEU cc_start: 0.8756 (mt) cc_final: 0.8306 (pp) REVERT: D 356 MET cc_start: 0.8094 (mtm) cc_final: 0.7889 (mtm) REVERT: D 408 MET cc_start: 0.2429 (mtt) cc_final: 0.0150 (ttp) REVERT: D 524 THR cc_start: 0.5410 (OUTLIER) cc_final: 0.5196 (t) outliers start: 19 outliers final: 11 residues processed: 87 average time/residue: 0.2852 time to fit residues: 35.7252 Evaluate side-chains 69 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 339 HIS Chi-restraints excluded: chain D residue 474 CYS Chi-restraints excluded: chain D residue 524 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 43 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 10 optimal weight: 0.0870 chunk 97 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 HIS D 287 HIS D 330 GLN D 339 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.102393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.069194 restraints weight = 48652.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068089 restraints weight = 27779.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.068077 restraints weight = 21666.026| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10233 Z= 0.214 Angle : 0.675 10.925 13956 Z= 0.338 Chirality : 0.045 0.172 1542 Planarity : 0.005 0.060 1777 Dihedral : 6.844 59.955 1510 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.21 % Allowed : 16.41 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.03 (0.24), residues: 1231 helix: 1.07 (0.52), residues: 104 sheet: 0.37 (0.22), residues: 526 loop : -0.51 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 45 HIS 0.008 0.001 HIS D 339 PHE 0.019 0.002 PHE C 75 TYR 0.017 0.002 TYR D 36 ARG 0.006 0.001 ARG C 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00641 ( 4) link_NAG-ASN : angle 3.02196 ( 12) link_BETA1-4 : bond 0.00475 ( 3) link_BETA1-4 : angle 2.67931 ( 9) link_ALPHA1-3 : bond 0.00573 ( 1) link_ALPHA1-3 : angle 2.09691 ( 3) hydrogen bonds : bond 0.04691 ( 353) hydrogen bonds : angle 5.88448 ( 1062) SS BOND : bond 0.00255 ( 20) SS BOND : angle 1.03649 ( 40) covalent geometry : bond 0.00484 (10205) covalent geometry : angle 0.66424 (13892) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 59 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8338 (tpp) cc_final: 0.8089 (tpp) REVERT: A 51 ASP cc_start: 0.8695 (t0) cc_final: 0.8291 (t70) REVERT: A 270 SER cc_start: 0.9412 (OUTLIER) cc_final: 0.8991 (p) REVERT: B 39 LYS cc_start: 0.8610 (tttp) cc_final: 0.8357 (mtmm) REVERT: B 107 ASP cc_start: 0.8958 (p0) cc_final: 0.8638 (t0) REVERT: C 34 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7865 (pt) REVERT: C 41 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7541 (tp) REVERT: C 44 MET cc_start: 0.8125 (tpp) cc_final: 0.7623 (mmm) REVERT: C 65 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7062 (t-90) REVERT: C 99 MET cc_start: 0.8930 (mmm) cc_final: 0.7940 (mmt) REVERT: C 126 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8479 (p0) REVERT: C 142 MET cc_start: 0.8820 (mpp) cc_final: 0.8356 (mpp) REVERT: C 184 ASP cc_start: 0.9299 (m-30) cc_final: 0.8811 (t0) REVERT: D 136 SER cc_start: 0.8646 (m) cc_final: 0.8257 (t) REVERT: D 143 LEU cc_start: 0.8705 (mt) cc_final: 0.8184 (pp) REVERT: D 256 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8852 (pp) REVERT: D 408 MET cc_start: 0.2281 (mtt) cc_final: 0.0555 (ttp) REVERT: D 524 THR cc_start: 0.5489 (p) cc_final: 0.5158 (t) outliers start: 35 outliers final: 20 residues processed: 87 average time/residue: 0.2497 time to fit residues: 32.5652 Evaluate side-chains 79 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 474 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 110 optimal weight: 30.0000 chunk 80 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 114 optimal weight: 50.0000 chunk 45 optimal weight: 2.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.101355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.068136 restraints weight = 48836.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.067038 restraints weight = 28606.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.066871 restraints weight = 22702.676| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10233 Z= 0.252 Angle : 0.700 12.780 13956 Z= 0.350 Chirality : 0.045 0.213 1542 Planarity : 0.005 0.048 1777 Dihedral : 5.977 57.771 1510 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.94 % Allowed : 16.59 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.23 (0.24), residues: 1231 helix: 0.86 (0.52), residues: 101 sheet: 0.17 (0.21), residues: 547 loop : -0.57 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 401 HIS 0.008 0.001 HIS A 216 PHE 0.013 0.002 PHE A 273 TYR 0.021 0.002 TYR D 36 ARG 0.004 0.001 ARG C 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 4) link_NAG-ASN : angle 2.99632 ( 12) link_BETA1-4 : bond 0.00810 ( 3) link_BETA1-4 : angle 2.82270 ( 9) link_ALPHA1-3 : bond 0.00418 ( 1) link_ALPHA1-3 : angle 2.77572 ( 3) hydrogen bonds : bond 0.04704 ( 353) hydrogen bonds : angle 5.84499 ( 1062) SS BOND : bond 0.00352 ( 20) SS BOND : angle 1.00178 ( 40) covalent geometry : bond 0.00568 (10205) covalent geometry : angle 0.68936 (13892) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 51 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8326 (tpp) cc_final: 0.8080 (tpp) REVERT: A 250 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7882 (ttt90) REVERT: A 270 SER cc_start: 0.9384 (OUTLIER) cc_final: 0.8956 (p) REVERT: B 39 LYS cc_start: 0.8630 (tttp) cc_final: 0.8425 (mtmm) REVERT: B 107 ASP cc_start: 0.8825 (p0) cc_final: 0.8426 (t0) REVERT: C 34 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8039 (pt) REVERT: C 65 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6710 (t-90) REVERT: C 99 MET cc_start: 0.8853 (mmm) cc_final: 0.7906 (mmt) REVERT: C 142 MET cc_start: 0.8901 (mpp) cc_final: 0.8338 (mpp) REVERT: C 184 ASP cc_start: 0.9331 (m-30) cc_final: 0.8728 (t0) REVERT: C 186 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7798 (mm) REVERT: D 136 SER cc_start: 0.8714 (m) cc_final: 0.8337 (t) REVERT: D 256 LEU cc_start: 0.9142 (tt) cc_final: 0.8926 (pp) REVERT: D 356 MET cc_start: 0.8074 (mtm) cc_final: 0.7721 (mmm) REVERT: D 408 MET cc_start: 0.2609 (mtt) cc_final: 0.0749 (tmm) REVERT: D 419 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8526 (m-80) outliers start: 43 outliers final: 24 residues processed: 88 average time/residue: 0.1970 time to fit residues: 25.9841 Evaluate side-chains 77 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 47 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 474 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 74 optimal weight: 0.2980 chunk 111 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS B 170 GLN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.101312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.067578 restraints weight = 48812.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.066556 restraints weight = 28396.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.066617 restraints weight = 20176.875| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10233 Z= 0.202 Angle : 0.649 13.014 13956 Z= 0.321 Chirality : 0.044 0.187 1542 Planarity : 0.005 0.060 1777 Dihedral : 5.793 59.736 1510 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.22 % Allowed : 17.05 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.23 (0.24), residues: 1231 helix: 1.00 (0.53), residues: 101 sheet: 0.17 (0.22), residues: 529 loop : -0.57 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 45 HIS 0.005 0.001 HIS C 65 PHE 0.010 0.002 PHE A 140 TYR 0.018 0.002 TYR D 357 ARG 0.005 0.001 ARG C 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 4) link_NAG-ASN : angle 2.84577 ( 12) link_BETA1-4 : bond 0.00479 ( 3) link_BETA1-4 : angle 2.32818 ( 9) link_ALPHA1-3 : bond 0.00576 ( 1) link_ALPHA1-3 : angle 1.77386 ( 3) hydrogen bonds : bond 0.04323 ( 353) hydrogen bonds : angle 5.69179 ( 1062) SS BOND : bond 0.00319 ( 20) SS BOND : angle 1.04050 ( 40) covalent geometry : bond 0.00459 (10205) covalent geometry : angle 0.63974 (13892) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 50 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8306 (tpp) cc_final: 0.8029 (tpp) REVERT: A 270 SER cc_start: 0.9447 (OUTLIER) cc_final: 0.9027 (p) REVERT: B 39 LYS cc_start: 0.8657 (tttp) cc_final: 0.8427 (mtmm) REVERT: B 107 ASP cc_start: 0.8799 (p0) cc_final: 0.8426 (t0) REVERT: C 34 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7971 (pt) REVERT: C 44 MET cc_start: 0.7852 (tpp) cc_final: 0.7500 (mmm) REVERT: C 65 HIS cc_start: 0.7416 (OUTLIER) cc_final: 0.6810 (t-90) REVERT: C 99 MET cc_start: 0.8875 (mmm) cc_final: 0.7900 (mmt) REVERT: C 142 MET cc_start: 0.8954 (mpp) cc_final: 0.8711 (mpp) REVERT: C 184 ASP cc_start: 0.9359 (m-30) cc_final: 0.8775 (t0) REVERT: C 186 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7723 (mm) REVERT: D 136 SER cc_start: 0.8686 (m) cc_final: 0.8303 (t) REVERT: D 356 MET cc_start: 0.8063 (mtm) cc_final: 0.7704 (mmm) REVERT: D 408 MET cc_start: 0.2695 (mtt) cc_final: 0.0736 (tmm) REVERT: D 419 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8515 (m-80) outliers start: 46 outliers final: 28 residues processed: 91 average time/residue: 0.1880 time to fit residues: 25.9993 Evaluate side-chains 81 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 48 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 474 CYS Chi-restraints excluded: chain D residue 518 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.101713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.068888 restraints weight = 48891.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.067869 restraints weight = 27308.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.067874 restraints weight = 20247.171| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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 0.039 10233 Z= 0.149 Angle : 0.599 9.303 13956 Z= 0.298 Chirality : 0.043 0.151 1542 Planarity : 0.005 0.072 1777 Dihedral : 5.529 59.141 1510 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.12 % Allowed : 19.16 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.04 (0.24), residues: 1231 helix: 1.19 (0.52), residues: 104 sheet: 0.32 (0.22), residues: 522 loop : -0.49 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 466 HIS 0.004 0.001 HIS C 65 PHE 0.011 0.001 PHE A 140 TYR 0.016 0.001 TYR D 36 ARG 0.007 0.000 ARG A 301 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 4) link_NAG-ASN : angle 2.67252 ( 12) link_BETA1-4 : bond 0.00250 ( 3) link_BETA1-4 : angle 1.93392 ( 9) link_ALPHA1-3 : bond 0.00706 ( 1) link_ALPHA1-3 : angle 1.47686 ( 3) hydrogen bonds : bond 0.03973 ( 353) hydrogen bonds : angle 5.48935 ( 1062) SS BOND : bond 0.00319 ( 20) SS BOND : angle 0.96481 ( 40) covalent geometry : bond 0.00340 (10205) covalent geometry : angle 0.59095 (13892) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 52 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: A 45 MET cc_start: 0.8266 (tpp) cc_final: 0.7981 (tpp) REVERT: A 270 SER cc_start: 0.9428 (OUTLIER) cc_final: 0.9023 (p) REVERT: B 39 LYS cc_start: 0.8642 (tttp) cc_final: 0.8373 (mtmm) REVERT: B 107 ASP cc_start: 0.8737 (p0) cc_final: 0.8418 (t0) REVERT: B 170 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8177 (mt0) REVERT: C 34 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7917 (pt) REVERT: C 65 HIS cc_start: 0.7287 (OUTLIER) cc_final: 0.6652 (t-90) REVERT: C 99 MET cc_start: 0.8878 (mmm) cc_final: 0.7912 (mmt) REVERT: C 142 MET cc_start: 0.8876 (mpp) cc_final: 0.8327 (mpp) REVERT: C 184 ASP cc_start: 0.9343 (m-30) cc_final: 0.8756 (t0) REVERT: C 186 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7699 (mm) REVERT: C 204 MET cc_start: 0.8366 (tpp) cc_final: 0.7867 (tpp) REVERT: D 136 SER cc_start: 0.8665 (m) cc_final: 0.8292 (t) REVERT: D 356 MET cc_start: 0.8132 (mtm) cc_final: 0.7774 (mmm) REVERT: D 408 MET cc_start: 0.2687 (mtt) cc_final: 0.0809 (tmm) outliers start: 34 outliers final: 24 residues processed: 82 average time/residue: 0.1855 time to fit residues: 23.5686 Evaluate side-chains 79 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 49 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 474 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 30.0000 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 67 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 116 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.101147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.068543 restraints weight = 50078.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.067392 restraints weight = 28879.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.067236 restraints weight = 22528.846| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10233 Z= 0.186 Angle : 0.630 12.976 13956 Z= 0.315 Chirality : 0.043 0.154 1542 Planarity : 0.005 0.079 1777 Dihedral : 5.755 59.800 1510 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.12 % Allowed : 18.70 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.10 (0.24), residues: 1231 helix: 1.14 (0.53), residues: 101 sheet: 0.33 (0.23), residues: 509 loop : -0.54 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 45 HIS 0.005 0.001 HIS C 65 PHE 0.013 0.002 PHE B 109 TYR 0.018 0.002 TYR D 36 ARG 0.009 0.001 ARG C 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 4) link_NAG-ASN : angle 2.84291 ( 12) link_BETA1-4 : bond 0.00426 ( 3) link_BETA1-4 : angle 2.17435 ( 9) link_ALPHA1-3 : bond 0.00597 ( 1) link_ALPHA1-3 : angle 1.66035 ( 3) hydrogen bonds : bond 0.04125 ( 353) hydrogen bonds : angle 5.57205 ( 1062) SS BOND : bond 0.00319 ( 20) SS BOND : angle 1.38831 ( 40) covalent geometry : bond 0.00429 (10205) covalent geometry : angle 0.61855 (13892) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 50 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: A 45 MET cc_start: 0.8217 (tpp) cc_final: 0.7936 (tpp) REVERT: A 120 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7162 (mt0) REVERT: A 270 SER cc_start: 0.9343 (OUTLIER) cc_final: 0.8948 (p) REVERT: B 170 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8202 (mt0) REVERT: C 34 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7996 (pt) REVERT: C 65 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.6564 (t-90) REVERT: C 99 MET cc_start: 0.8870 (mmm) cc_final: 0.7870 (mmt) REVERT: C 142 MET cc_start: 0.8995 (mpp) cc_final: 0.8545 (mpp) REVERT: C 184 ASP cc_start: 0.9342 (m-30) cc_final: 0.8745 (t0) REVERT: C 186 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7702 (mm) REVERT: C 204 MET cc_start: 0.8471 (tpp) cc_final: 0.8075 (tpp) REVERT: D 136 SER cc_start: 0.8702 (m) cc_final: 0.8322 (t) REVERT: D 356 MET cc_start: 0.8092 (mtm) cc_final: 0.7727 (mmm) REVERT: D 408 MET cc_start: 0.2853 (mtt) cc_final: 0.0533 (tmm) outliers start: 45 outliers final: 30 residues processed: 90 average time/residue: 0.1843 time to fit residues: 25.5013 Evaluate side-chains 84 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 47 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 474 CYS Chi-restraints excluded: chain D residue 535 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 85 optimal weight: 0.0010 chunk 78 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 33 optimal weight: 0.0070 overall best weight: 2.8010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.100518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.068497 restraints weight = 50055.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.066703 restraints weight = 30526.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.066408 restraints weight = 25101.057| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10233 Z= 0.211 Angle : 0.645 11.612 13956 Z= 0.321 Chirality : 0.044 0.164 1542 Planarity : 0.005 0.079 1777 Dihedral : 5.750 59.563 1510 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.40 % Allowed : 19.07 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.21 (0.24), residues: 1231 helix: 0.97 (0.51), residues: 101 sheet: 0.15 (0.22), residues: 523 loop : -0.50 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 466 HIS 0.005 0.001 HIS C 65 PHE 0.015 0.002 PHE B 109 TYR 0.023 0.002 TYR D 282 ARG 0.011 0.001 ARG C 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 4) link_NAG-ASN : angle 2.96772 ( 12) link_BETA1-4 : bond 0.00556 ( 3) link_BETA1-4 : angle 2.24416 ( 9) link_ALPHA1-3 : bond 0.00538 ( 1) link_ALPHA1-3 : angle 1.70465 ( 3) hydrogen bonds : bond 0.04262 ( 353) hydrogen bonds : angle 5.54151 ( 1062) SS BOND : bond 0.00348 ( 20) SS BOND : angle 0.92910 ( 40) covalent geometry : bond 0.00481 (10205) covalent geometry : angle 0.63510 (13892) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 48 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: A 45 MET cc_start: 0.8315 (tpp) cc_final: 0.7986 (tpp) REVERT: A 120 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7216 (mt0) REVERT: A 270 SER cc_start: 0.9402 (OUTLIER) cc_final: 0.8999 (p) REVERT: B 170 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8150 (mt0) REVERT: C 34 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8015 (pt) REVERT: C 65 HIS cc_start: 0.7153 (OUTLIER) cc_final: 0.6426 (t-90) REVERT: C 99 MET cc_start: 0.8845 (mmm) cc_final: 0.7847 (mmt) REVERT: C 142 MET cc_start: 0.9044 (mpp) cc_final: 0.8527 (mpp) REVERT: C 184 ASP cc_start: 0.9393 (m-30) cc_final: 0.8831 (t0) REVERT: C 186 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7825 (mm) REVERT: C 204 MET cc_start: 0.8653 (tpp) cc_final: 0.8369 (tpp) REVERT: D 136 SER cc_start: 0.8678 (m) cc_final: 0.8303 (t) REVERT: D 356 MET cc_start: 0.8154 (mtm) cc_final: 0.7800 (mmm) REVERT: D 408 MET cc_start: 0.3541 (mtt) cc_final: 0.1150 (tmm) REVERT: D 419 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8403 (m-10) outliers start: 48 outliers final: 34 residues processed: 90 average time/residue: 0.1703 time to fit residues: 24.4205 Evaluate side-chains 89 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 47 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 144 CYS Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 474 CYS Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 535 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 114 optimal weight: 50.0000 chunk 108 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 HIS D 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.100752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.068301 restraints weight = 49787.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.066627 restraints weight = 27978.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.066614 restraints weight = 21440.521| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10233 Z= 0.183 Angle : 0.624 10.976 13956 Z= 0.309 Chirality : 0.043 0.151 1542 Planarity : 0.005 0.080 1777 Dihedral : 5.664 57.646 1510 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.48 % Allowed : 19.62 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.17 (0.24), residues: 1231 helix: 1.01 (0.51), residues: 101 sheet: 0.22 (0.22), residues: 513 loop : -0.52 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 466 HIS 0.005 0.001 HIS C 65 PHE 0.014 0.002 PHE B 109 TYR 0.019 0.002 TYR D 36 ARG 0.013 0.001 ARG C 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 4) link_NAG-ASN : angle 2.80344 ( 12) link_BETA1-4 : bond 0.00439 ( 3) link_BETA1-4 : angle 2.01402 ( 9) link_ALPHA1-3 : bond 0.00599 ( 1) link_ALPHA1-3 : angle 1.49955 ( 3) hydrogen bonds : bond 0.04098 ( 353) hydrogen bonds : angle 5.48648 ( 1062) SS BOND : bond 0.00351 ( 20) SS BOND : angle 0.93206 ( 40) covalent geometry : bond 0.00420 (10205) covalent geometry : angle 0.61518 (13892) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 48 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: A 45 MET cc_start: 0.8209 (tpp) cc_final: 0.7889 (tpp) REVERT: A 120 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7246 (mt0) REVERT: A 270 SER cc_start: 0.9355 (OUTLIER) cc_final: 0.8967 (p) REVERT: B 170 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8134 (mt0) REVERT: C 34 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7929 (pt) REVERT: C 44 MET cc_start: 0.7804 (tpp) cc_final: 0.7391 (mmt) REVERT: C 65 HIS cc_start: 0.7125 (OUTLIER) cc_final: 0.6430 (t-90) REVERT: C 99 MET cc_start: 0.8836 (mmm) cc_final: 0.7858 (mmt) REVERT: C 142 MET cc_start: 0.9035 (mpp) cc_final: 0.8511 (mpp) REVERT: C 184 ASP cc_start: 0.9393 (m-30) cc_final: 0.8840 (t0) REVERT: C 186 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7886 (mm) REVERT: D 136 SER cc_start: 0.8661 (m) cc_final: 0.8287 (t) REVERT: D 356 MET cc_start: 0.8153 (mtm) cc_final: 0.7838 (mmm) REVERT: D 408 MET cc_start: 0.3952 (mtt) cc_final: 0.1430 (tmm) outliers start: 38 outliers final: 29 residues processed: 80 average time/residue: 0.1772 time to fit residues: 22.7787 Evaluate side-chains 82 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 46 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 474 CYS Chi-restraints excluded: chain D residue 535 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 0.9990 chunk 90 optimal weight: 0.0370 chunk 69 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 35 optimal weight: 0.3980 chunk 52 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 101 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.101296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.069091 restraints weight = 49254.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.067810 restraints weight = 29487.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.067408 restraints weight = 23428.709| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10233 Z= 0.132 Angle : 0.604 11.366 13956 Z= 0.297 Chirality : 0.042 0.148 1542 Planarity : 0.005 0.087 1777 Dihedral : 5.400 55.854 1510 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.75 % Allowed : 20.53 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.02 (0.24), residues: 1231 helix: 1.32 (0.51), residues: 101 sheet: 0.28 (0.22), residues: 513 loop : -0.41 (0.27), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 466 HIS 0.004 0.001 HIS C 65 PHE 0.011 0.001 PHE B 109 TYR 0.017 0.001 TYR D 36 ARG 0.013 0.000 ARG C 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 4) link_NAG-ASN : angle 2.53659 ( 12) link_BETA1-4 : bond 0.00247 ( 3) link_BETA1-4 : angle 1.68730 ( 9) link_ALPHA1-3 : bond 0.00699 ( 1) link_ALPHA1-3 : angle 1.23553 ( 3) hydrogen bonds : bond 0.03851 ( 353) hydrogen bonds : angle 5.35740 ( 1062) SS BOND : bond 0.00307 ( 20) SS BOND : angle 0.90998 ( 40) covalent geometry : bond 0.00307 (10205) covalent geometry : angle 0.59736 (13892) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 48 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 SER cc_start: 0.9377 (OUTLIER) cc_final: 0.8967 (p) REVERT: C 44 MET cc_start: 0.7817 (tpp) cc_final: 0.7399 (mmt) REVERT: C 65 HIS cc_start: 0.7295 (OUTLIER) cc_final: 0.6630 (t-90) REVERT: C 99 MET cc_start: 0.8853 (mmm) cc_final: 0.7881 (mmt) REVERT: C 142 MET cc_start: 0.9040 (mpp) cc_final: 0.8542 (mpp) REVERT: C 184 ASP cc_start: 0.9343 (m-30) cc_final: 0.8764 (t0) REVERT: C 186 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7731 (mm) REVERT: C 204 MET cc_start: 0.8406 (tpp) cc_final: 0.8009 (tpp) REVERT: D 136 SER cc_start: 0.8615 (m) cc_final: 0.8250 (t) REVERT: D 356 MET cc_start: 0.8149 (mtm) cc_final: 0.7851 (mmm) REVERT: D 408 MET cc_start: 0.3197 (mtt) cc_final: 0.1095 (tmm) REVERT: D 524 THR cc_start: 0.6249 (p) cc_final: 0.5850 (t) outliers start: 30 outliers final: 27 residues processed: 72 average time/residue: 0.1733 time to fit residues: 19.9865 Evaluate side-chains 78 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 48 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 474 CYS Chi-restraints excluded: chain D residue 535 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 85 optimal weight: 0.0170 chunk 84 optimal weight: 1.9990 chunk 109 optimal weight: 50.0000 chunk 9 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.100939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.066016 restraints weight = 48668.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.066070 restraints weight = 25958.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.066258 restraints weight = 16326.395| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10233 Z= 0.142 Angle : 0.602 11.392 13956 Z= 0.294 Chirality : 0.042 0.148 1542 Planarity : 0.005 0.087 1777 Dihedral : 5.312 56.148 1510 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.66 % Allowed : 20.71 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.01 (0.24), residues: 1231 helix: 1.40 (0.51), residues: 103 sheet: 0.31 (0.22), residues: 519 loop : -0.43 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 466 HIS 0.005 0.001 HIS C 65 PHE 0.011 0.001 PHE B 109 TYR 0.017 0.001 TYR D 36 ARG 0.015 0.001 ARG C 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 4) link_NAG-ASN : angle 2.61936 ( 12) link_BETA1-4 : bond 0.00321 ( 3) link_BETA1-4 : angle 1.85414 ( 9) link_ALPHA1-3 : bond 0.00587 ( 1) link_ALPHA1-3 : angle 1.33183 ( 3) hydrogen bonds : bond 0.03832 ( 353) hydrogen bonds : angle 5.30196 ( 1062) SS BOND : bond 0.00301 ( 20) SS BOND : angle 0.87209 ( 40) covalent geometry : bond 0.00330 (10205) covalent geometry : angle 0.59394 (13892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4030.58 seconds wall clock time: 71 minutes 23.57 seconds (4283.57 seconds total)