Starting phenix.real_space_refine on Sat Sep 12 13:10:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z14_14440/09_2026/7z14_14440.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z14_14440/09_2026/7z14_14440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z14_14440/09_2026/7z14_14440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z14_14440/09_2026/7z14_14440.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z14_14440/09_2026/7z14_14440.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z14_14440/09_2026/7z14_14440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z14_14440/09_2026/7z14_14440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z14_14440/09_2026/7z14_14440.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.058 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 95 5.16 5 C 10337 2.51 5 N 2515 2.21 5 O 2909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15856 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2892 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 335} Chain breaks: 4 Chain: "B" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3018 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 350} Chain breaks: 2 Chain: "C" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3046 Classifications: {'peptide': 376} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 349} Chain breaks: 1 Chain: "D" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2669 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "E" Number of atoms: 2945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2945 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain breaks: 1 Chain: "F" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 471 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "G" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 471 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.53, per 1000 atoms: 0.22 Number of scatterers: 15856 At special positions: 0 Unit cell: (101.905, 129.385, 135.11, 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 95 16.00 O 2909 8.00 N 2515 7.00 C 10337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.06 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.05 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 22 " distance=2.03 Simple disulfide: pdb=" SG CYS F 17 " - pdb=" SG CYS F 39 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 52 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 22 " distance=2.03 Simple disulfide: pdb=" SG CYS G 17 " - pdb=" SG CYS G 39 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 52 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 58 " 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 ALPHA1-2 " MAN H 5 " - " MAN H 6 " " MAN H 8 " - " MAN H 9 " " MAN K 5 " - " MAN K 6 " " MAN K 8 " - " MAN K 9 " ALPHA1-3 " BMA H 3 " - " MAN H 8 " " MAN H 4 " - " MAN H 7 " " BMA K 3 " - " MAN K 8 " " MAN K 4 " - " MAN K 7 " ALPHA1-6 " BMA H 3 " - " MAN H 4 " " MAN H 4 " - " MAN H 5 " " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 5 " " NAG L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 5 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " NAG L 3 " NAG-ASN " NAG C 601 " - " ASN C 208 " " NAG H 1 " - " ASN D 141 " " NAG I 1 " - " ASN C 143 " " NAG J 1 " - " ASN B 141 " " NAG K 1 " - " ASN A 141 " " NAG L 1 " - " ASN E 141 " Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 719.5 milliseconds 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3682 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 27 sheets defined 35.6% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.518A pdb=" N ASP A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 85 " --> pdb=" O SER A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 81 through 85' Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 219 through 230 removed outlier: 3.867A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 241 through 264 Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.606A pdb=" N MET A 324 " --> pdb=" O PRO A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 426 removed outlier: 3.660A pdb=" N PHE A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.587A pdb=" N VAL B 85 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 241 Proline residue: B 227 - end of helix removed outlier: 4.571A pdb=" N PHE B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 247 through 270 removed outlier: 4.093A pdb=" N ASP B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 307 Processing helix chain 'B' and resid 315 through 323 removed outlier: 3.512A pdb=" N ARG B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 460 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 233 through 246 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 255 through 276 removed outlier: 3.694A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 314 Processing helix chain 'C' and resid 443 through 476 Proline residue: C 463 - end of helix Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.632A pdb=" N LEU D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.136A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 218 through 230 removed outlier: 3.672A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 241 through 264 Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 400 through 425 Processing helix chain 'E' and resid 2 through 13 removed outlier: 3.996A pdb=" N ARG E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.866A pdb=" N SER E 66 " --> pdb=" O TYR E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 81 through 85 Processing helix chain 'E' and resid 131 through 135 removed outlier: 4.335A pdb=" N TYR E 134 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 226 removed outlier: 3.727A pdb=" N ILE E 223 " --> pdb=" O PRO E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.675A pdb=" N VAL E 240 " --> pdb=" O VAL E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 271 removed outlier: 3.835A pdb=" N GLN E 271 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 Processing helix chain 'E' and resid 440 through 473 removed outlier: 3.763A pdb=" N TRP E 453 " --> pdb=" O LYS E 449 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE E 454 " --> pdb=" O ALA E 450 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN E 473 " --> pdb=" O THR E 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 78 removed outlier: 4.140A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE A 61 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASP A 30 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL A 29 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N SER A 159 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE A 31 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 44 removed outlier: 7.461A pdb=" N ILE A 38 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N ARG A 55 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU A 40 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN A 53 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.474A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.474A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP A 180 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 80 removed outlier: 4.367A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 80 removed outlier: 4.367A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASN B 53 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU B 40 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N PHE B 55 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR B 38 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASN B 57 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR B 36 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ALA B 59 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N GLY B 34 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR B 61 " --> pdb=" O ARG B 32 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N ARG B 32 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 139 through 140 removed outlier: 7.109A pdb=" N GLN B 214 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE B 188 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 82 removed outlier: 3.524A pdb=" N LEU C 82 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 82 removed outlier: 3.524A pdb=" N LEU C 82 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR C 51 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER C 44 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN C 55 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR C 63 " --> pdb=" O ASN C 32 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASN C 32 " --> pdb=" O TYR C 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AB3, first strand: chain 'C' and resid 141 through 143 removed outlier: 6.946A pdb=" N ILE C 220 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 164 through 166 Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 78 removed outlier: 4.334A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 77 through 78 removed outlier: 4.334A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE D 49 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER D 42 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN D 53 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE D 61 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP D 30 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 90 through 92 removed outlier: 4.492A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 90 through 92 removed outlier: 4.492A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR D 196 " --> pdb=" O TYR D 190 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR D 190 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP D 180 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.597A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 37 through 44 removed outlier: 5.719A pdb=" N LEU E 37 " --> pdb=" O TRP E 55 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TRP E 55 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR E 51 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU E 43 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA E 49 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 78 through 80 Processing sheet with id=AC3, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.135A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 139 through 142 removed outlier: 6.819A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 162 through 163 Processing sheet with id=AC6, first strand: chain 'F' and resid 2 through 4 removed outlier: 3.889A pdb=" N CYS F 3 " --> pdb=" O LYS F 15 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 33 through 39 Processing sheet with id=AC8, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=AC9, first strand: chain 'G' and resid 22 through 28 removed outlier: 3.665A pdb=" N TYR G 23 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY G 38 " --> pdb=" O TYR G 23 " (cutoff:3.500A) 727 hydrogen bonds defined for protein. 2037 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 5290 1.38 - 1.53: 9015 1.53 - 1.68: 1825 1.68 - 1.83: 141 1.83 - 1.98: 2 Bond restraints: 16273 Sorted by residual: bond pdb=" CB CYS A 192 " pdb=" SG CYS A 192 " ideal model delta sigma weight residual 1.808 1.634 0.174 3.30e-02 9.18e+02 2.79e+01 bond pdb=" CB CYS A 193 " pdb=" SG CYS A 193 " ideal model delta sigma weight residual 1.808 1.982 -0.174 3.30e-02 9.18e+02 2.78e+01 bond pdb=" CB CYS D 192 " pdb=" SG CYS D 192 " ideal model delta sigma weight residual 1.808 1.891 -0.083 3.30e-02 9.18e+02 6.36e+00 bond pdb=" CA CYS A 193 " pdb=" CB CYS A 193 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.22e-02 6.72e+03 3.24e+00 bond pdb=" CA CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sigma weight residual 1.530 1.505 0.026 1.58e-02 4.01e+03 2.62e+00 ... (remaining 16268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.55: 22194 6.55 - 13.09: 14 13.09 - 19.64: 1 19.64 - 26.19: 0 26.19 - 32.74: 1 Bond angle restraints: 22210 Sorted by residual: angle pdb=" CA CYS A 192 " pdb=" CB CYS A 192 " pdb=" SG CYS A 192 " ideal model delta sigma weight residual 114.40 147.14 -32.74 2.30e+00 1.89e-01 2.03e+02 angle pdb=" C CYS A 192 " pdb=" CA CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sigma weight residual 110.92 97.35 13.57 1.59e+00 3.96e-01 7.29e+01 angle pdb=" CA CYS A 193 " pdb=" CB CYS A 193 " pdb=" SG CYS A 193 " ideal model delta sigma weight residual 114.40 127.08 -12.68 2.30e+00 1.89e-01 3.04e+01 angle pdb=" CA CYS D 192 " pdb=" CB CYS D 192 " pdb=" SG CYS D 192 " ideal model delta sigma weight residual 114.40 122.90 -8.50 2.30e+00 1.89e-01 1.37e+01 angle pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N CYS A 193 " ideal model delta sigma weight residual 116.79 112.83 3.96 1.28e+00 6.10e-01 9.58e+00 ... (remaining 22205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 8616 17.06 - 34.12: 700 34.12 - 51.18: 112 51.18 - 68.24: 27 68.24 - 85.30: 12 Dihedral angle restraints: 9467 sinusoidal: 3808 harmonic: 5659 Sorted by residual: dihedral pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N CYS A 193 " pdb=" CA CYS A 193 " ideal model delta harmonic sigma weight residual -180.00 -111.65 -68.35 0 5.00e+00 4.00e-02 1.87e+02 dihedral pdb=" CB CYS C 130 " pdb=" SG CYS C 130 " pdb=" SG CYS C 144 " pdb=" CB CYS C 144 " ideal model delta sinusoidal sigma weight residual -86.00 -17.92 -68.08 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CB CYS G 17 " pdb=" SG CYS G 17 " pdb=" SG CYS G 39 " pdb=" CB CYS G 39 " ideal model delta sinusoidal sigma weight residual 93.00 158.67 -65.67 1 1.00e+01 1.00e-02 5.64e+01 ... (remaining 9464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2251 0.062 - 0.123: 380 0.123 - 0.185: 30 0.185 - 0.247: 1 0.247 - 0.308: 3 Chirality restraints: 2665 Sorted by residual: chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 141 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2662 not shown) Planarity restraints: 2709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 222 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.06e+00 pdb=" C VAL B 222 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL B 222 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR B 223 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 327 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO B 328 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 328 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 328 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 216 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO B 217 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " -0.027 5.00e-02 4.00e+02 ... (remaining 2706 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 285 2.68 - 3.24: 15343 3.24 - 3.79: 24956 3.79 - 4.35: 33829 4.35 - 4.90: 56492 Nonbonded interactions: 130905 Sorted by model distance: nonbonded pdb=" O TYR C 248 " pdb=" ND2 ASN D 297 " model vdw 2.128 3.120 nonbonded pdb=" NH2 ARG E 147 " pdb=" OE1 GLU E 208 " model vdw 2.139 3.120 nonbonded pdb=" OG SER A 239 " pdb=" NE2 HIS B 306 " model vdw 2.241 3.120 nonbonded pdb=" OH TYR F 23 " pdb=" OE2 GLU F 36 " model vdw 2.241 3.040 nonbonded pdb=" O VAL A 285 " pdb=" OG SER A 288 " model vdw 2.248 3.040 ... (remaining 130900 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 301 or resid 399 through 425)) selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.380 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.460 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 16316 Z= 0.175 Angle : 0.745 32.737 22324 Z= 0.349 Chirality : 0.046 0.308 2665 Planarity : 0.004 0.052 2703 Dihedral : 12.895 85.303 5740 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.20), residues: 1881 helix: 1.39 (0.21), residues: 576 sheet: -0.33 (0.26), residues: 437 loop : -0.86 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 147 TYR 0.017 0.001 TYR C 218 PHE 0.028 0.001 PHE D 233 TRP 0.011 0.001 TRP B 317 HIS 0.005 0.001 HIS D 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (16273) covalent geometry : angle 0.71890 / 0.34 (22210) SS BOND : bond 0.00978 / 0.49 ( 15) SS BOND : angle 4.35640 / 2.29 ( 30) hydrogen bonds : bond 0.17301 / 11.78 ( 686) hydrogen bonds : angle 7.11469 / 5.09 ( 2037) link_ALPHA1-2 : bond 0.00224 / 0.11 ( 4) link_ALPHA1-2 : angle 1.91107 / 1.10 ( 12) link_ALPHA1-3 : bond 0.00190 / 0.09 ( 4) link_ALPHA1-3 : angle 1.95357 / 1.16 ( 12) link_ALPHA1-6 : bond 0.00325 / 0.17 ( 6) link_ALPHA1-6 : angle 1.99862 / 1.20 ( 18) link_BETA1-4 : bond 0.00356 / 0.23 ( 8) link_BETA1-4 : angle 1.66276 / 1.00 ( 24) link_NAG-ASN : bond 0.00271 / 0.14 ( 6) link_NAG-ASN : angle 2.61211 / 1.46 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.597 Fit side-chains REVERT: A 193 CYS cc_start: 0.5925 (m) cc_final: 0.5435 (m) REVERT: B 133 MET cc_start: 0.7196 (tmm) cc_final: 0.6614 (tmm) REVERT: B 320 GLN cc_start: 0.7043 (pp30) cc_final: 0.6756 (pp30) REVERT: C 46 LYS cc_start: 0.7598 (pptt) cc_final: 0.6692 (pptt) REVERT: C 247 PHE cc_start: 0.8205 (m-10) cc_final: 0.7796 (m-80) REVERT: D 175 GLU cc_start: 0.7549 (pm20) cc_final: 0.7165 (pm20) REVERT: D 227 PHE cc_start: 0.7968 (t80) cc_final: 0.7571 (t80) REVERT: D 238 ASP cc_start: 0.8408 (m-30) cc_final: 0.8167 (m-30) REVERT: D 415 MET cc_start: 0.7428 (mmp) cc_final: 0.6423 (ttt) REVERT: E 116 MET cc_start: 0.8436 (mmt) cc_final: 0.8088 (mmt) REVERT: E 130 ILE cc_start: 0.8883 (mm) cc_final: 0.8617 (mm) REVERT: E 199 LEU cc_start: 0.8366 (tt) cc_final: 0.8163 (tt) REVERT: E 236 LEU cc_start: 0.8903 (mt) cc_final: 0.8657 (mt) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.1121 time to fit residues: 58.9286 Evaluate side-chains 267 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.0030 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 ASN E 159 GLN F 10 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103490 restraints weight = 23301.019| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.61 r_work: 0.3139 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16316 Z= 0.141 Angle : 0.618 8.611 22324 Z= 0.307 Chirality : 0.044 0.172 2665 Planarity : 0.004 0.047 2703 Dihedral : 4.794 58.088 2047 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.24 % Allowed : 8.13 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.20), residues: 1881 helix: 1.49 (0.21), residues: 583 sheet: -0.30 (0.26), residues: 447 loop : -0.76 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 20 TYR 0.015 0.001 TYR C 248 PHE 0.028 0.001 PHE B 262 TRP 0.013 0.001 TRP D 187 HIS 0.005 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (16273) covalent geometry : angle 0.60295 / 0.30 (22210) SS BOND : bond 0.00851 / 0.43 ( 15) SS BOND : angle 2.57680 / 1.44 ( 30) hydrogen bonds : bond 0.04015 / 2.71 ( 686) hydrogen bonds : angle 5.23333 / 3.73 ( 2037) link_ALPHA1-2 : bond 0.00155 / 0.08 ( 4) link_ALPHA1-2 : angle 1.81824 / 1.06 ( 12) link_ALPHA1-3 : bond 0.00461 / 0.23 ( 4) link_ALPHA1-3 : angle 1.61572 / 0.97 ( 12) link_ALPHA1-6 : bond 0.00440 / 0.25 ( 6) link_ALPHA1-6 : angle 1.67199 / 1.03 ( 18) link_BETA1-4 : bond 0.00175 / 0.10 ( 8) link_BETA1-4 : angle 1.52195 / 0.96 ( 24) link_NAG-ASN : bond 0.00315 / 0.16 ( 6) link_NAG-ASN : angle 2.19455 / 1.20 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 284 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 324 MET cc_start: 0.4774 (tmm) cc_final: 0.3638 (mtt) REVERT: B 133 MET cc_start: 0.7674 (tmm) cc_final: 0.6700 (tmm) REVERT: B 198 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7879 (mtm180) REVERT: B 253 ILE cc_start: 0.8797 (mm) cc_final: 0.8539 (mm) REVERT: C 46 LYS cc_start: 0.7927 (pptt) cc_final: 0.7717 (pptt) REVERT: C 171 ASP cc_start: 0.8436 (m-30) cc_final: 0.7367 (p0) REVERT: C 471 PHE cc_start: 0.7816 (t80) cc_final: 0.7558 (t80) REVERT: D 224 LEU cc_start: 0.8171 (tp) cc_final: 0.7956 (tp) REVERT: D 227 PHE cc_start: 0.8067 (t80) cc_final: 0.7761 (t80) REVERT: D 234 TYR cc_start: 0.7924 (t80) cc_final: 0.7594 (t80) REVERT: D 238 ASP cc_start: 0.8481 (m-30) cc_final: 0.8234 (m-30) REVERT: D 415 MET cc_start: 0.7654 (mmp) cc_final: 0.6515 (ttt) REVERT: E 130 ILE cc_start: 0.8952 (mm) cc_final: 0.8696 (mm) REVERT: E 147 ARG cc_start: 0.8932 (ptt180) cc_final: 0.8663 (ptt180) REVERT: E 199 LEU cc_start: 0.8386 (tt) cc_final: 0.8115 (tt) REVERT: E 236 LEU cc_start: 0.8995 (mt) cc_final: 0.8779 (mt) REVERT: E 300 ASN cc_start: 0.8172 (t0) cc_final: 0.7713 (t0) outliers start: 22 outliers final: 12 residues processed: 295 average time/residue: 0.1047 time to fit residues: 48.4044 Evaluate side-chains 272 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 260 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain G residue 17 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 177 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 125 optimal weight: 0.0020 chunk 106 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 175 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 58 GLN D 297 ASN E 159 GLN E 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.123540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103394 restraints weight = 23682.144| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.64 r_work: 0.3135 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16316 Z= 0.128 Angle : 0.587 9.369 22324 Z= 0.288 Chirality : 0.044 0.209 2665 Planarity : 0.004 0.046 2703 Dihedral : 4.638 54.668 2047 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.69 % Allowed : 11.01 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.20), residues: 1881 helix: 1.68 (0.21), residues: 578 sheet: -0.32 (0.25), residues: 448 loop : -0.77 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.016 0.001 TYR C 218 PHE 0.018 0.001 PHE B 262 TRP 0.013 0.001 TRP D 187 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (16273) covalent geometry : angle 0.57204 / 0.28 (22210) SS BOND : bond 0.00774 / 0.39 ( 15) SS BOND : angle 2.49743 / 1.37 ( 30) hydrogen bonds : bond 0.03673 / 2.49 ( 686) hydrogen bonds : angle 4.79076 / 3.41 ( 2037) link_ALPHA1-2 : bond 0.00279 / 0.14 ( 4) link_ALPHA1-2 : angle 1.63096 / 0.95 ( 12) link_ALPHA1-3 : bond 0.00386 / 0.19 ( 4) link_ALPHA1-3 : angle 1.55714 / 0.93 ( 12) link_ALPHA1-6 : bond 0.00337 / 0.19 ( 6) link_ALPHA1-6 : angle 1.55070 / 0.94 ( 18) link_BETA1-4 : bond 0.00216 / 0.13 ( 8) link_BETA1-4 : angle 1.53053 / 0.94 ( 24) link_NAG-ASN : bond 0.00211 / 0.11 ( 6) link_NAG-ASN : angle 2.07546 / 1.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 283 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 172 GLU cc_start: 0.7968 (pm20) cc_final: 0.7736 (pt0) REVERT: A 277 TYR cc_start: 0.8539 (t80) cc_final: 0.8148 (t80) REVERT: A 278 MET cc_start: 0.7681 (tmm) cc_final: 0.7452 (tpp) REVERT: A 324 MET cc_start: 0.4499 (tmm) cc_final: 0.3237 (mtt) REVERT: B 77 ASP cc_start: 0.8585 (p0) cc_final: 0.8136 (p0) REVERT: B 133 MET cc_start: 0.7809 (tmm) cc_final: 0.6599 (tmm) REVERT: B 253 ILE cc_start: 0.8742 (mm) cc_final: 0.8412 (mm) REVERT: C 171 ASP cc_start: 0.8306 (m-30) cc_final: 0.7317 (p0) REVERT: C 471 PHE cc_start: 0.7833 (t80) cc_final: 0.7564 (t80) REVERT: D 175 GLU cc_start: 0.7873 (pm20) cc_final: 0.7389 (pm20) REVERT: D 224 LEU cc_start: 0.8216 (tp) cc_final: 0.7806 (tt) REVERT: D 227 PHE cc_start: 0.7896 (t80) cc_final: 0.7503 (t80) REVERT: D 238 ASP cc_start: 0.8475 (m-30) cc_final: 0.8228 (m-30) REVERT: E 116 MET cc_start: 0.8807 (mmt) cc_final: 0.8603 (mmt) REVERT: E 130 ILE cc_start: 0.8967 (mm) cc_final: 0.8681 (mm) REVERT: E 147 ARG cc_start: 0.8908 (ptt180) cc_final: 0.8574 (ptp-170) REVERT: E 199 LEU cc_start: 0.8413 (tt) cc_final: 0.8104 (tt) REVERT: F 15 LYS cc_start: 0.8908 (ptpt) cc_final: 0.8263 (pttp) outliers start: 30 outliers final: 15 residues processed: 300 average time/residue: 0.1114 time to fit residues: 51.9898 Evaluate side-chains 272 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 257 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 451 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 13 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 214 GLN E 159 GLN E 300 ASN E 439 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.122253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102086 restraints weight = 23631.145| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.64 r_work: 0.3117 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16316 Z= 0.149 Angle : 0.592 10.758 22324 Z= 0.293 Chirality : 0.044 0.200 2665 Planarity : 0.004 0.047 2703 Dihedral : 4.809 56.081 2047 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.75 % Allowed : 12.70 % Favored : 85.54 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.20), residues: 1881 helix: 1.74 (0.21), residues: 583 sheet: -0.38 (0.25), residues: 443 loop : -0.73 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 282 TYR 0.009 0.001 TYR D 72 PHE 0.026 0.001 PHE B 262 TRP 0.012 0.001 TRP D 187 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (16273) covalent geometry : angle 0.57576 / 0.29 (22210) SS BOND : bond 0.01146 / 0.57 ( 15) SS BOND : angle 2.67538 / 1.53 ( 30) hydrogen bonds : bond 0.03539 / 2.39 ( 686) hydrogen bonds : angle 4.63692 / 3.30 ( 2037) link_ALPHA1-2 : bond 0.00196 / 0.10 ( 4) link_ALPHA1-2 : angle 1.67930 / 0.98 ( 12) link_ALPHA1-3 : bond 0.00257 / 0.13 ( 4) link_ALPHA1-3 : angle 1.55139 / 0.93 ( 12) link_ALPHA1-6 : bond 0.00337 / 0.18 ( 6) link_ALPHA1-6 : angle 1.56506 / 0.97 ( 18) link_BETA1-4 : bond 0.00163 / 0.10 ( 8) link_BETA1-4 : angle 1.60709 / 0.98 ( 24) link_NAG-ASN : bond 0.00286 / 0.14 ( 6) link_NAG-ASN : angle 2.11709 / 1.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 265 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 277 TYR cc_start: 0.8614 (t80) cc_final: 0.8164 (t80) REVERT: A 278 MET cc_start: 0.7656 (tmm) cc_final: 0.7374 (tpp) REVERT: B 77 ASP cc_start: 0.8571 (p0) cc_final: 0.8121 (p0) REVERT: B 133 MET cc_start: 0.7960 (tmm) cc_final: 0.6601 (tmm) REVERT: B 253 ILE cc_start: 0.8776 (mm) cc_final: 0.8420 (mm) REVERT: C 46 LYS cc_start: 0.8018 (pptt) cc_final: 0.7688 (pptt) REVERT: C 171 ASP cc_start: 0.8301 (m-30) cc_final: 0.7276 (p0) REVERT: C 172 TYR cc_start: 0.6947 (p90) cc_final: 0.6718 (p90) REVERT: C 471 PHE cc_start: 0.7864 (t80) cc_final: 0.7574 (t80) REVERT: D 224 LEU cc_start: 0.8175 (tp) cc_final: 0.7799 (tt) REVERT: D 227 PHE cc_start: 0.7916 (t80) cc_final: 0.7544 (t80) REVERT: D 238 ASP cc_start: 0.8512 (m-30) cc_final: 0.8306 (m-30) REVERT: D 243 MET cc_start: 0.8421 (tpp) cc_final: 0.8104 (mmm) REVERT: D 415 MET cc_start: 0.7928 (mmp) cc_final: 0.6624 (ttt) REVERT: E 130 ILE cc_start: 0.8990 (mm) cc_final: 0.8706 (mm) REVERT: E 147 ARG cc_start: 0.8901 (ptt180) cc_final: 0.8650 (ptt180) REVERT: E 199 LEU cc_start: 0.8432 (tt) cc_final: 0.8103 (tt) REVERT: E 271 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8301 (mt0) REVERT: F 15 LYS cc_start: 0.8915 (ptpt) cc_final: 0.8277 (pttp) outliers start: 31 outliers final: 19 residues processed: 281 average time/residue: 0.1058 time to fit residues: 47.0244 Evaluate side-chains 277 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 257 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 271 GLN Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 55 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 151 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 15 optimal weight: 0.0050 chunk 68 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 305 ASN C 447 ASN E 159 GLN E 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.100868 restraints weight = 23605.657| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.64 r_work: 0.3097 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 16316 Z= 0.168 Angle : 0.606 11.837 22324 Z= 0.300 Chirality : 0.045 0.232 2665 Planarity : 0.004 0.048 2703 Dihedral : 4.867 59.966 2047 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.60 % Allowed : 13.61 % Favored : 83.79 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.20), residues: 1881 helix: 1.73 (0.21), residues: 583 sheet: -0.38 (0.25), residues: 441 loop : -0.74 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.011 0.001 TYR C 218 PHE 0.016 0.001 PHE B 262 TRP 0.011 0.001 TRP A 187 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (16273) covalent geometry : angle 0.58995 / 0.29 (22210) SS BOND : bond 0.00762 / 0.38 ( 15) SS BOND : angle 2.64503 / 1.51 ( 30) hydrogen bonds : bond 0.03576 / 2.41 ( 686) hydrogen bonds : angle 4.58156 / 3.27 ( 2037) link_ALPHA1-2 : bond 0.00179 / 0.09 ( 4) link_ALPHA1-2 : angle 1.70065 / 0.99 ( 12) link_ALPHA1-3 : bond 0.00241 / 0.12 ( 4) link_ALPHA1-3 : angle 1.58690 / 0.96 ( 12) link_ALPHA1-6 : bond 0.00371 / 0.20 ( 6) link_ALPHA1-6 : angle 1.58211 / 0.97 ( 18) link_BETA1-4 : bond 0.00147 / 0.09 ( 8) link_BETA1-4 : angle 1.68847 / 1.02 ( 24) link_NAG-ASN : bond 0.00345 / 0.18 ( 6) link_NAG-ASN : angle 2.16747 / 1.20 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 179 LYS cc_start: 0.8783 (mmtp) cc_final: 0.8573 (mttt) REVERT: A 277 TYR cc_start: 0.8642 (t80) cc_final: 0.8172 (t80) REVERT: A 278 MET cc_start: 0.7645 (tmm) cc_final: 0.7196 (tpt) REVERT: B 77 ASP cc_start: 0.8526 (p0) cc_final: 0.8043 (p0) REVERT: B 133 MET cc_start: 0.8005 (tmm) cc_final: 0.6879 (tmm) REVERT: B 253 ILE cc_start: 0.8796 (mm) cc_final: 0.8446 (mm) REVERT: C 45 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7915 (tt) REVERT: C 46 LYS cc_start: 0.7920 (pptt) cc_final: 0.7703 (pptt) REVERT: C 171 ASP cc_start: 0.8309 (m-30) cc_final: 0.7272 (p0) REVERT: C 172 TYR cc_start: 0.6869 (p90) cc_final: 0.6630 (p90) REVERT: C 471 PHE cc_start: 0.7854 (t80) cc_final: 0.7524 (t80) REVERT: D 175 GLU cc_start: 0.8034 (pm20) cc_final: 0.7823 (pm20) REVERT: D 224 LEU cc_start: 0.8151 (tp) cc_final: 0.7705 (tp) REVERT: D 227 PHE cc_start: 0.7834 (t80) cc_final: 0.7404 (t80) REVERT: E 130 ILE cc_start: 0.9045 (mm) cc_final: 0.8791 (mm) REVERT: E 147 ARG cc_start: 0.8951 (ptt180) cc_final: 0.8677 (ptt180) REVERT: E 199 LEU cc_start: 0.8421 (tt) cc_final: 0.8093 (tt) REVERT: E 271 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8398 (mt0) REVERT: F 15 LYS cc_start: 0.8952 (ptpt) cc_final: 0.8317 (pttp) outliers start: 46 outliers final: 25 residues processed: 291 average time/residue: 0.1072 time to fit residues: 49.4463 Evaluate side-chains 278 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 251 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 271 GLN Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 55 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 188 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 0.0670 chunk 71 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 214 GLN E 159 GLN E 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102445 restraints weight = 23474.266| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.65 r_work: 0.3123 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 16316 Z= 0.128 Angle : 0.594 13.180 22324 Z= 0.294 Chirality : 0.044 0.249 2665 Planarity : 0.004 0.049 2703 Dihedral : 4.827 62.989 2047 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.54 % Allowed : 14.85 % Favored : 82.61 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.20), residues: 1881 helix: 1.84 (0.21), residues: 578 sheet: -0.36 (0.26), residues: 443 loop : -0.74 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.012 0.001 TYR C 218 PHE 0.015 0.001 PHE B 262 TRP 0.011 0.001 TRP A 187 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (16273) covalent geometry : angle 0.57448 / 0.29 (22210) SS BOND : bond 0.00974 / 0.49 ( 15) SS BOND : angle 3.20880 / 2.23 ( 30) hydrogen bonds : bond 0.03396 / 2.29 ( 686) hydrogen bonds : angle 4.45634 / 3.18 ( 2037) link_ALPHA1-2 : bond 0.00272 / 0.13 ( 4) link_ALPHA1-2 : angle 1.60071 / 0.93 ( 12) link_ALPHA1-3 : bond 0.00346 / 0.17 ( 4) link_ALPHA1-3 : angle 1.49527 / 0.90 ( 12) link_ALPHA1-6 : bond 0.00359 / 0.19 ( 6) link_ALPHA1-6 : angle 1.51828 / 0.94 ( 18) link_BETA1-4 : bond 0.00148 / 0.08 ( 8) link_BETA1-4 : angle 1.55276 / 0.96 ( 24) link_NAG-ASN : bond 0.00199 / 0.10 ( 6) link_NAG-ASN : angle 2.03840 / 1.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 274 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 179 LYS cc_start: 0.8755 (mmtp) cc_final: 0.8532 (mttt) REVERT: A 277 TYR cc_start: 0.8672 (t80) cc_final: 0.8225 (t80) REVERT: A 278 MET cc_start: 0.7587 (tmm) cc_final: 0.7164 (tpt) REVERT: B 77 ASP cc_start: 0.8444 (p0) cc_final: 0.8079 (p0) REVERT: B 133 MET cc_start: 0.7997 (tmm) cc_final: 0.6869 (tmm) REVERT: B 253 ILE cc_start: 0.8764 (mm) cc_final: 0.8406 (mm) REVERT: C 171 ASP cc_start: 0.8291 (m-30) cc_final: 0.7268 (p0) REVERT: C 172 TYR cc_start: 0.6885 (p90) cc_final: 0.6644 (p90) REVERT: C 471 PHE cc_start: 0.7875 (t80) cc_final: 0.7580 (t80) REVERT: D 13 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7884 (pt0) REVERT: D 175 GLU cc_start: 0.8013 (pm20) cc_final: 0.7533 (pm20) REVERT: D 224 LEU cc_start: 0.8140 (tp) cc_final: 0.7870 (tp) REVERT: D 227 PHE cc_start: 0.7875 (t80) cc_final: 0.7541 (t80) REVERT: D 415 MET cc_start: 0.7915 (mmp) cc_final: 0.6568 (ttt) REVERT: E 130 ILE cc_start: 0.9022 (mm) cc_final: 0.8753 (mm) REVERT: E 147 ARG cc_start: 0.8930 (ptt180) cc_final: 0.8651 (ptt180) REVERT: E 199 LEU cc_start: 0.8385 (tt) cc_final: 0.8052 (tt) REVERT: E 271 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8418 (mt0) REVERT: E 295 MET cc_start: 0.8248 (mmm) cc_final: 0.7815 (ttp) REVERT: F 15 LYS cc_start: 0.8927 (ptpt) cc_final: 0.8278 (pttp) outliers start: 45 outliers final: 24 residues processed: 304 average time/residue: 0.1084 time to fit residues: 52.3320 Evaluate side-chains 283 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 271 GLN Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain F residue 13 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 57 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 182 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 214 GLN E 159 GLN E 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.122889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102642 restraints weight = 23338.078| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.65 r_work: 0.3125 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 16316 Z= 0.132 Angle : 0.603 14.525 22324 Z= 0.297 Chirality : 0.044 0.286 2665 Planarity : 0.004 0.049 2703 Dihedral : 4.850 64.785 2047 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.03 % Allowed : 15.87 % Favored : 82.10 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.20), residues: 1881 helix: 1.85 (0.21), residues: 578 sheet: -0.33 (0.26), residues: 443 loop : -0.73 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.025 0.001 TYR C 218 PHE 0.019 0.001 PHE D 284 TRP 0.014 0.001 TRP A 311 HIS 0.005 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (16273) covalent geometry : angle 0.58461 / 0.29 (22210) SS BOND : bond 0.01211 / 0.60 ( 15) SS BOND : angle 3.18773 / 2.01 ( 30) hydrogen bonds : bond 0.03359 / 2.27 ( 686) hydrogen bonds : angle 4.40585 / 3.14 ( 2037) link_ALPHA1-2 : bond 0.00259 / 0.13 ( 4) link_ALPHA1-2 : angle 1.61375 / 0.94 ( 12) link_ALPHA1-3 : bond 0.00333 / 0.17 ( 4) link_ALPHA1-3 : angle 1.50432 / 0.90 ( 12) link_ALPHA1-6 : bond 0.00314 / 0.17 ( 6) link_ALPHA1-6 : angle 1.49974 / 0.93 ( 18) link_BETA1-4 : bond 0.00193 / 0.12 ( 8) link_BETA1-4 : angle 1.57046 / 0.97 ( 24) link_NAG-ASN : bond 0.00218 / 0.11 ( 6) link_NAG-ASN : angle 2.04571 / 1.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 277 TYR cc_start: 0.8698 (t80) cc_final: 0.8273 (t80) REVERT: A 278 MET cc_start: 0.7788 (tmm) cc_final: 0.7481 (tpp) REVERT: B 50 MET cc_start: 0.8620 (ttp) cc_final: 0.8386 (ttp) REVERT: B 77 ASP cc_start: 0.8455 (p0) cc_final: 0.8089 (p0) REVERT: B 133 MET cc_start: 0.8016 (tmm) cc_final: 0.6748 (tmm) REVERT: B 253 ILE cc_start: 0.8717 (mm) cc_final: 0.8398 (mm) REVERT: C 172 TYR cc_start: 0.6878 (p90) cc_final: 0.6601 (p90) REVERT: C 471 PHE cc_start: 0.7803 (t80) cc_final: 0.7509 (t80) REVERT: D 13 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7821 (pt0) REVERT: D 175 GLU cc_start: 0.8029 (pm20) cc_final: 0.7545 (pm20) REVERT: D 224 LEU cc_start: 0.8136 (tp) cc_final: 0.7589 (tp) REVERT: D 227 PHE cc_start: 0.7849 (t80) cc_final: 0.7434 (t80) REVERT: E 130 ILE cc_start: 0.9019 (mm) cc_final: 0.8749 (mm) REVERT: E 147 ARG cc_start: 0.8936 (ptt180) cc_final: 0.8671 (ptt180) REVERT: E 199 LEU cc_start: 0.8378 (tt) cc_final: 0.8040 (tt) REVERT: E 295 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7935 (mmm) REVERT: F 15 LYS cc_start: 0.8906 (ptpt) cc_final: 0.8209 (pttp) outliers start: 36 outliers final: 24 residues processed: 296 average time/residue: 0.1017 time to fit residues: 47.9687 Evaluate side-chains 288 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 263 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 55 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 142 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 GLN B 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099541 restraints weight = 23784.453| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.65 r_work: 0.3077 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 16316 Z= 0.209 Angle : 0.673 16.762 22324 Z= 0.332 Chirality : 0.046 0.293 2665 Planarity : 0.004 0.049 2703 Dihedral : 5.067 74.287 2047 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.15 % Allowed : 16.04 % Favored : 81.82 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 1881 helix: 1.78 (0.21), residues: 578 sheet: -0.31 (0.26), residues: 444 loop : -0.83 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 20 TYR 0.021 0.001 TYR C 218 PHE 0.013 0.001 PHE D 135 TRP 0.017 0.001 TRP A 311 HIS 0.006 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.21 (16273) covalent geometry : angle 0.64436 / 0.32 (22210) SS BOND : bond 0.01347 / 0.66 ( 15) SS BOND : angle 4.45628 / 2.47 ( 30) hydrogen bonds : bond 0.03568 / 2.38 ( 686) hydrogen bonds : angle 4.47888 / 3.20 ( 2037) link_ALPHA1-2 : bond 0.00173 / 0.08 ( 4) link_ALPHA1-2 : angle 1.75321 / 1.03 ( 12) link_ALPHA1-3 : bond 0.00190 / 0.10 ( 4) link_ALPHA1-3 : angle 1.61786 / 0.98 ( 12) link_ALPHA1-6 : bond 0.00398 / 0.21 ( 6) link_ALPHA1-6 : angle 1.61598 / 0.99 ( 18) link_BETA1-4 : bond 0.00175 / 0.11 ( 8) link_BETA1-4 : angle 1.79602 / 1.06 ( 24) link_NAG-ASN : bond 0.00441 / 0.23 ( 6) link_NAG-ASN : angle 2.21982 / 1.23 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 264 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 277 TYR cc_start: 0.8794 (t80) cc_final: 0.8315 (t80) REVERT: A 278 MET cc_start: 0.7625 (tmm) cc_final: 0.7185 (tpt) REVERT: B 50 MET cc_start: 0.8723 (ttp) cc_final: 0.8490 (ttp) REVERT: B 77 ASP cc_start: 0.8573 (p0) cc_final: 0.8064 (p0) REVERT: B 133 MET cc_start: 0.8120 (tmm) cc_final: 0.6843 (tmm) REVERT: B 253 ILE cc_start: 0.8761 (mm) cc_final: 0.8467 (mm) REVERT: C 172 TYR cc_start: 0.6923 (p90) cc_final: 0.6607 (p90) REVERT: C 471 PHE cc_start: 0.7878 (t80) cc_final: 0.7538 (t80) REVERT: D 13 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7848 (pt0) REVERT: D 175 GLU cc_start: 0.8128 (pm20) cc_final: 0.7916 (pm20) REVERT: D 224 LEU cc_start: 0.8152 (tp) cc_final: 0.7738 (tp) REVERT: D 227 PHE cc_start: 0.8012 (t80) cc_final: 0.7491 (t80) REVERT: E 130 ILE cc_start: 0.9061 (mm) cc_final: 0.8823 (mm) REVERT: E 147 ARG cc_start: 0.8922 (ptt180) cc_final: 0.8656 (ptt180) REVERT: E 199 LEU cc_start: 0.8386 (tt) cc_final: 0.8027 (tt) REVERT: E 295 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7924 (mmm) REVERT: E 300 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7973 (t0) REVERT: F 15 LYS cc_start: 0.8878 (ptpt) cc_final: 0.8116 (pttp) outliers start: 38 outliers final: 29 residues processed: 287 average time/residue: 0.1012 time to fit residues: 46.6898 Evaluate side-chains 283 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 252 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 55 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 104 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101565 restraints weight = 23315.899| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.53 r_work: 0.3122 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 16316 Z= 0.138 Angle : 0.628 14.408 22324 Z= 0.310 Chirality : 0.044 0.285 2665 Planarity : 0.004 0.049 2703 Dihedral : 4.971 74.181 2047 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.03 % Allowed : 16.37 % Favored : 81.59 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1881 helix: 1.84 (0.21), residues: 578 sheet: -0.32 (0.26), residues: 437 loop : -0.80 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.019 0.001 TYR C 218 PHE 0.020 0.001 PHE B 262 TRP 0.016 0.001 TRP A 311 HIS 0.006 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (16273) covalent geometry : angle 0.60359 / 0.30 (22210) SS BOND : bond 0.01139 / 0.59 ( 15) SS BOND : angle 3.95477 / 2.16 ( 30) hydrogen bonds : bond 0.03387 / 2.28 ( 686) hydrogen bonds : angle 4.39722 / 3.13 ( 2037) link_ALPHA1-2 : bond 0.00289 / 0.14 ( 4) link_ALPHA1-2 : angle 1.57484 / 0.91 ( 12) link_ALPHA1-3 : bond 0.00348 / 0.18 ( 4) link_ALPHA1-3 : angle 1.48100 / 0.89 ( 12) link_ALPHA1-6 : bond 0.00360 / 0.19 ( 6) link_ALPHA1-6 : angle 1.49425 / 0.93 ( 18) link_BETA1-4 : bond 0.00167 / 0.10 ( 8) link_BETA1-4 : angle 1.55260 / 0.97 ( 24) link_NAG-ASN : bond 0.00217 / 0.12 ( 6) link_NAG-ASN : angle 2.12054 / 1.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 265 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 277 TYR cc_start: 0.8755 (t80) cc_final: 0.8304 (t80) REVERT: A 278 MET cc_start: 0.7632 (tmm) cc_final: 0.7334 (tpp) REVERT: B 77 ASP cc_start: 0.8758 (p0) cc_final: 0.8289 (p0) REVERT: B 133 MET cc_start: 0.8018 (tmm) cc_final: 0.6688 (tmm) REVERT: B 253 ILE cc_start: 0.8755 (mm) cc_final: 0.8464 (mm) REVERT: B 429 GLN cc_start: 0.7967 (mt0) cc_final: 0.7607 (mt0) REVERT: C 172 TYR cc_start: 0.6896 (p90) cc_final: 0.6627 (p90) REVERT: C 471 PHE cc_start: 0.7812 (t80) cc_final: 0.7509 (t80) REVERT: D 13 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7804 (pt0) REVERT: D 175 GLU cc_start: 0.8167 (pm20) cc_final: 0.7672 (pm20) REVERT: D 224 LEU cc_start: 0.8154 (tp) cc_final: 0.7492 (tp) REVERT: D 227 PHE cc_start: 0.7998 (t80) cc_final: 0.7542 (t80) REVERT: E 130 ILE cc_start: 0.9013 (mm) cc_final: 0.8808 (mm) REVERT: E 199 LEU cc_start: 0.8280 (tt) cc_final: 0.7909 (tt) REVERT: E 295 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7841 (mmm) REVERT: F 15 LYS cc_start: 0.8821 (ptpt) cc_final: 0.8039 (pttp) REVERT: G 1 MET cc_start: 0.5856 (ppp) cc_final: 0.5372 (ptm) outliers start: 36 outliers final: 28 residues processed: 287 average time/residue: 0.1065 time to fit residues: 49.1039 Evaluate side-chains 280 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 55 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 181 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.121508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102100 restraints weight = 23308.400| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.53 r_work: 0.3129 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 16316 Z= 0.147 Angle : 0.670 22.173 22324 Z= 0.327 Chirality : 0.044 0.315 2665 Planarity : 0.004 0.049 2703 Dihedral : 4.937 77.246 2047 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.98 % Allowed : 16.94 % Favored : 81.08 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.20), residues: 1881 helix: 1.86 (0.21), residues: 578 sheet: -0.21 (0.26), residues: 436 loop : -0.82 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.018 0.001 TYR C 218 PHE 0.016 0.001 PHE B 262 TRP 0.017 0.001 TRP A 311 HIS 0.007 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.15 (16273) covalent geometry : angle 0.63765 / 0.31 (22210) SS BOND : bond 0.01218 / 0.60 ( 15) SS BOND : angle 5.03372 / 2.66 ( 30) hydrogen bonds : bond 0.03333 / 2.24 ( 686) hydrogen bonds : angle 4.35081 / 3.10 ( 2037) link_ALPHA1-2 : bond 0.00271 / 0.13 ( 4) link_ALPHA1-2 : angle 1.60390 / 0.94 ( 12) link_ALPHA1-3 : bond 0.00335 / 0.17 ( 4) link_ALPHA1-3 : angle 1.50166 / 0.90 ( 12) link_ALPHA1-6 : bond 0.00341 / 0.19 ( 6) link_ALPHA1-6 : angle 1.49498 / 0.93 ( 18) link_BETA1-4 : bond 0.00157 / 0.09 ( 8) link_BETA1-4 : angle 1.55761 / 0.98 ( 24) link_NAG-ASN : bond 0.00227 / 0.13 ( 6) link_NAG-ASN : angle 2.10697 / 1.16 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3762 Ramachandran restraints generated. 1881 Oldfield, 0 Emsley, 1881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 260 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 277 TYR cc_start: 0.8729 (t80) cc_final: 0.8277 (t80) REVERT: A 278 MET cc_start: 0.7604 (tmm) cc_final: 0.7396 (tpp) REVERT: B 77 ASP cc_start: 0.8705 (p0) cc_final: 0.8244 (p0) REVERT: B 133 MET cc_start: 0.8041 (tmm) cc_final: 0.6660 (tmm) REVERT: B 167 GLU cc_start: 0.7375 (mp0) cc_final: 0.7114 (mp0) REVERT: B 253 ILE cc_start: 0.8751 (mm) cc_final: 0.8430 (mm) REVERT: B 429 GLN cc_start: 0.7971 (mt0) cc_final: 0.7630 (mt0) REVERT: C 172 TYR cc_start: 0.6885 (p90) cc_final: 0.6625 (p90) REVERT: C 471 PHE cc_start: 0.7797 (t80) cc_final: 0.7508 (t80) REVERT: D 13 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7811 (pt0) REVERT: D 175 GLU cc_start: 0.8166 (pm20) cc_final: 0.7657 (pm20) REVERT: D 224 LEU cc_start: 0.8183 (tp) cc_final: 0.7533 (tp) REVERT: D 227 PHE cc_start: 0.7998 (t80) cc_final: 0.7528 (t80) REVERT: D 243 MET cc_start: 0.8416 (tpp) cc_final: 0.8137 (mmm) REVERT: E 130 ILE cc_start: 0.9067 (mm) cc_final: 0.8856 (mm) REVERT: E 199 LEU cc_start: 0.8289 (tt) cc_final: 0.7929 (tt) REVERT: E 295 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7833 (mmm) REVERT: F 15 LYS cc_start: 0.8815 (ptpt) cc_final: 0.8026 (pttp) outliers start: 35 outliers final: 28 residues processed: 282 average time/residue: 0.0962 time to fit residues: 43.9254 Evaluate side-chains 284 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 255 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 55 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 188 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 0.0060 chunk 71 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 39 ASN ** 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 = 0.3519 r_free = 0.3519 target = 0.123659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103431 restraints weight = 23340.584| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.63 r_work: 0.3134 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 16316 Z= 0.144 Angle : 0.668 20.647 22324 Z= 0.326 Chirality : 0.044 0.312 2665 Planarity : 0.004 0.049 2703 Dihedral : 4.920 77.069 2047 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.98 % Allowed : 17.05 % Favored : 80.97 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1881 helix: 1.89 (0.21), residues: 578 sheet: -0.19 (0.26), residues: 438 loop : -0.80 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.018 0.001 TYR C 218 PHE 0.037 0.001 PHE B 262 TRP 0.017 0.001 TRP A 311 HIS 0.005 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.14 (16273) covalent geometry : angle 0.63556 / 0.31 (22210) SS BOND : bond 0.01129 / 0.56 ( 15) SS BOND : angle 4.99303 / 2.62 ( 30) hydrogen bonds : bond 0.03301 / 2.23 ( 686) hydrogen bonds : angle 4.32004 / 3.08 ( 2037) link_ALPHA1-2 : bond 0.00283 / 0.14 ( 4) link_ALPHA1-2 : angle 1.58487 / 0.92 ( 12) link_ALPHA1-3 : bond 0.00352 / 0.18 ( 4) link_ALPHA1-3 : angle 1.48735 / 0.89 ( 12) link_ALPHA1-6 : bond 0.00351 / 0.19 ( 6) link_ALPHA1-6 : angle 1.49967 / 0.93 ( 18) link_BETA1-4 : bond 0.00210 / 0.12 ( 8) link_BETA1-4 : angle 1.54482 / 0.97 ( 24) link_NAG-ASN : bond 0.00192 / 0.11 ( 6) link_NAG-ASN : angle 2.15151 / 1.19 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3291.42 seconds wall clock time: 57 minutes 39.16 seconds (3459.16 seconds total)