Starting phenix.real_space_refine on Sat Sep 12 16:00:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ql6_14065/09_2026/7ql6_14065.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ql6_14065/09_2026/7ql6_14065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ql6_14065/09_2026/7ql6_14065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ql6_14065/09_2026/7ql6_14065.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ql6_14065/09_2026/7ql6_14065.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ql6_14065/09_2026/7ql6_14065.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ql6_14065/09_2026/7ql6_14065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ql6_14065/09_2026/7ql6_14065.map" } resolution = 3.23 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= 0.002 sd= 0.043 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 83 5.16 5 C 10837 2.51 5 N 2603 2.21 5 O 3094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 16617 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3125 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 365} Chain breaks: 1 Chain: "B" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3292 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "C" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3466 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 399} Chain breaks: 1 Chain: "D" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2993 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 348} Chain breaks: 1 Chain: "E" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3280 Classifications: {'peptide': 404} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 382} Chain breaks: 1 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'CCE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'CCE': 1} Classifications: {'undetermined': 1} Chain: "E" 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: 3.33, per 1000 atoms: 0.20 Number of scatterers: 16617 At special positions: 0 Unit cell: (100.76, 104.195, 179.765, 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 83 16.00 O 3094 8.00 N 2603 7.00 C 10837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, 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=2.05 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 6 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 6 " " BMA L 3 " - " MAN L 6 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 5 " " BMA L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " 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 " - " BMA L 3 " NAG-ASN " NAG E 501 " - " ASN E 68 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 141 " " NAG H 1 " - " ASN C 143 " " NAG I 1 " - " ASN C 70 " " NAG J 1 " - " ASN C 208 " " NAG K 1 " - " ASN D 141 " " NAG L 1 " - " ASN E 141 " Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 765.4 milliseconds 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 20 sheets defined 41.3% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 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: 3.699A pdb=" N VAL A 85 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 232 removed outlier: 4.568A pdb=" N ILE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 262 Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 320 through 323 Processing helix chain 'A' and resid 380 through 431 removed outlier: 4.283A pdb=" N GLY A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 68 through 73 removed outlier: 4.246A pdb=" N GLU B 73 " --> pdb=" O ALA B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.652A pdb=" N VAL B 85 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 241 removed outlier: 4.522A pdb=" N ILE B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Proline residue: B 227 - end of helix removed outlier: 4.391A pdb=" N PHE B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 267 removed outlier: 3.929A pdb=" N SER B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 306 Processing helix chain 'B' and resid 315 through 324 removed outlier: 3.992A pdb=" N GLU B 324 " --> pdb=" O GLN B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 removed outlier: 4.220A pdb=" N PHE B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 460 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.869A pdb=" N SER C 75 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 245 removed outlier: 4.556A pdb=" N THR C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.667A pdb=" N LEU C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 249 Processing helix chain 'C' and resid 255 through 277 removed outlier: 3.722A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 315 removed outlier: 3.526A pdb=" N ARG C 315 " --> pdb=" O ASN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 416 through 478 Proline residue: C 463 - end of helix Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 218 through 230 removed outlier: 4.178A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 235 removed outlier: 4.343A pdb=" N TYR D 234 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 264 Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 309 through 319 removed outlier: 4.080A pdb=" N ILE D 317 " --> pdb=" O ARG D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 421 removed outlier: 4.496A pdb=" N GLU D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N HIS D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.254A pdb=" N GLU E 73 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 219 through 226 Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 243 removed outlier: 3.619A pdb=" N VAL E 240 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE E 242 " --> pdb=" O LEU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 271 Processing helix chain 'E' and resid 281 through 309 Processing helix chain 'E' and resid 318 through 327 Processing helix chain 'E' and resid 328 through 334 Processing helix chain 'E' and resid 420 through 470 removed outlier: 3.561A pdb=" N SER E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 118 Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 118 removed outlier: 6.404A pdb=" N ILE A 49 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A 43 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU A 51 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG A 55 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU A 37 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG A 57 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU A 35 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN A 59 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL A 33 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ILE A 61 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ILE A 31 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 80 Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.848A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP A 180 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.819A 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: 4.180A 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: 4.180A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLU B 49 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU B 43 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR B 51 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE B 55 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU B 37 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASN B 57 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU B 35 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA B 59 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL B 33 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N THR B 61 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL B 31 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.777A pdb=" N GLN B 214 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE B 188 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 82 Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 82 removed outlier: 6.239A pdb=" N THR C 51 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU C 45 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR C 53 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TRP C 57 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LEU C 39 " --> pdb=" O TRP C 57 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP C 59 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU C 37 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA C 61 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU C 35 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N TYR C 63 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE C 33 " --> pdb=" O TYR C 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.015A pdb=" N ALA C 150 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLN C 213 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG C 222 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE C 192 " --> pdb=" O ARG C 222 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.015A pdb=" N ALA C 150 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLN C 213 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 164 through 167 Processing sheet with id=AB5, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AB6, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.295A pdb=" N ILE D 49 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL D 43 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU D 51 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ARG D 55 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU D 37 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG D 57 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU D 35 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLN D 59 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL D 33 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N ILE D 61 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE D 31 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 91 through 92 removed outlier: 3.785A pdb=" N CYS D 142 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE D 205 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR D 198 " --> pdb=" O TRP D 187 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP D 187 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASP D 200 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS D 185 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR D 202 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY D 183 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS D 204 " --> pdb=" O TYR D 181 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR D 181 " --> pdb=" O HIS D 204 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE D 206 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.243A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.243A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA E 49 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU E 43 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR E 51 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP E 55 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LEU E 37 " --> pdb=" O TRP E 55 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU E 57 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU E 35 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLN E 59 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU E 33 " --> pdb=" O GLN E 59 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N ASN E 61 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL E 31 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.096A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.096A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) 867 hydrogen bonds defined for protein. 2517 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2598 1.32 - 1.46: 5259 1.46 - 1.59: 9060 1.59 - 1.73: 0 1.73 - 1.86: 135 Bond restraints: 17052 Sorted by residual: bond pdb=" C5 CCE A 601 " pdb=" N6 CCE A 601 " ideal model delta sigma weight residual 1.340 1.453 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C5 CCE D 601 " pdb=" N6 CCE D 601 " ideal model delta sigma weight residual 1.340 1.452 -0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" CA ALA D 96 " pdb=" CB ALA D 96 " ideal model delta sigma weight residual 1.537 1.479 0.058 1.67e-02 3.59e+03 1.21e+01 bond pdb=" C PRO E 479 " pdb=" O PRO E 479 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.30e-02 5.92e+03 1.21e+01 bond pdb=" C3 BMA G 3 " pdb=" O3 BMA G 3 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 1.01e+01 ... (remaining 17047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 22881 2.24 - 4.49: 312 4.49 - 6.73: 73 6.73 - 8.97: 4 8.97 - 11.22: 4 Bond angle restraints: 23274 Sorted by residual: angle pdb=" N PRO E 481 " pdb=" CA PRO E 481 " pdb=" C PRO E 481 " ideal model delta sigma weight residual 113.47 120.62 -7.15 1.43e+00 4.89e-01 2.50e+01 angle pdb=" N PHE B 468 " pdb=" CA PHE B 468 " pdb=" C PHE B 468 " ideal model delta sigma weight residual 113.56 107.05 6.51 1.39e+00 5.18e-01 2.20e+01 angle pdb=" C PRO B 467 " pdb=" CA PRO B 467 " pdb=" CB PRO B 467 " ideal model delta sigma weight residual 111.85 106.17 5.68 1.42e+00 4.96e-01 1.60e+01 angle pdb=" N ALA D 96 " pdb=" CA ALA D 96 " pdb=" C ALA D 96 " ideal model delta sigma weight residual 114.04 109.33 4.71 1.24e+00 6.50e-01 1.44e+01 angle pdb=" N TYR B 134 " pdb=" CA TYR B 134 " pdb=" CB TYR B 134 " ideal model delta sigma weight residual 114.10 110.32 3.78 1.00e+00 1.00e+00 1.43e+01 ... (remaining 23269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 9250 17.21 - 34.42: 489 34.42 - 51.63: 77 51.63 - 68.84: 19 68.84 - 86.04: 7 Dihedral angle restraints: 9842 sinusoidal: 3940 harmonic: 5902 Sorted by residual: dihedral pdb=" CA CYS A 142 " pdb=" C CYS A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA PHE B 137 " pdb=" C PHE B 137 " pdb=" N ASP B 138 " pdb=" CA ASP B 138 " ideal model delta harmonic sigma weight residual -180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA CYS D 192 " pdb=" C CYS D 192 " pdb=" N CYS D 193 " pdb=" CA CYS D 193 " ideal model delta harmonic sigma weight residual -180.00 -159.08 -20.92 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 9839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2417 0.064 - 0.127: 353 0.127 - 0.191: 21 0.191 - 0.255: 6 0.255 - 0.318: 9 Chirality restraints: 2806 Sorted by residual: chirality pdb=" CA VAL C 31 " pdb=" N VAL C 31 " pdb=" C VAL C 31 " pdb=" CB VAL C 31 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2803 not shown) Planarity restraints: 2837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 92 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C LEU D 92 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU D 92 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR D 93 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 121 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO C 122 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 122 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 122 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 215 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C VAL D 215 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL D 215 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL D 216 " 0.010 2.00e-02 2.50e+03 ... (remaining 2834 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3651 2.79 - 3.31: 16118 3.31 - 3.84: 28024 3.84 - 4.37: 33076 4.37 - 4.90: 57144 Nonbonded interactions: 138013 Sorted by model distance: nonbonded pdb=" O SER A 226 " pdb=" OG1 THR A 229 " model vdw 2.258 3.040 nonbonded pdb=" O SER D 226 " pdb=" OG1 THR D 229 " model vdw 2.263 3.040 nonbonded pdb=" O ILE A 315 " pdb=" OG1 THR A 319 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR B 220 " pdb=" OE2 GLU C 280 " model vdw 2.276 3.040 nonbonded pdb=" O GLY E 182 " pdb=" NZ LYS E 218 " model vdw 2.294 3.120 ... (remaining 138008 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 322 or resid 378 through 421 or resid 601)) selection = (chain 'D' and (resid 1 through 322 or resid 378 through 601)) } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.810 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 0.113 17095 Z= 0.232 Angle : 0.684 11.218 23396 Z= 0.338 Chirality : 0.048 0.318 2806 Planarity : 0.004 0.043 2829 Dihedral : 10.856 86.045 5981 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.60 % Allowed : 4.41 % Favored : 94.99 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.19), residues: 1970 helix: 2.24 (0.19), residues: 756 sheet: -0.42 (0.26), residues: 383 loop : -0.83 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 79 TYR 0.012 0.001 TYR D 93 PHE 0.015 0.001 PHE A 284 TRP 0.012 0.001 TRP B 139 HIS 0.003 0.001 HIS D 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.23 (17052) covalent geometry : angle 0.67065 / 0.33 (23274) SS BOND : bond 0.00867 / 0.43 ( 7) SS BOND : angle 2.79357 / 1.51 ( 14) hydrogen bonds : bond 0.11351 / 8.08 ( 793) hydrogen bonds : angle 5.32146 / 3.64 ( 2517) link_ALPHA1-3 : bond 0.00404 / 0.21 ( 6) link_ALPHA1-3 : angle 2.42297 / 1.91 ( 18) link_ALPHA1-6 : bond 0.00473 / 0.32 ( 9) link_ALPHA1-6 : angle 1.67005 / 1.09 ( 27) link_BETA1-4 : bond 0.00399 / 0.26 ( 13) link_BETA1-4 : angle 1.83869 / 1.18 ( 39) link_NAG-ASN : bond 0.00241 / 0.14 ( 8) link_NAG-ASN : angle 1.64672 / 1.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 360 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8486 (m-40) cc_final: 0.8017 (m110) REVERT: A 238 ASP cc_start: 0.7441 (t0) cc_final: 0.7205 (t0) REVERT: A 252 SER cc_start: 0.9239 (m) cc_final: 0.9016 (p) REVERT: B 250 SER cc_start: 0.8933 (t) cc_final: 0.8694 (m) REVERT: B 442 VAL cc_start: 0.8220 (t) cc_final: 0.7923 (p) REVERT: C 296 MET cc_start: 0.7766 (mtp) cc_final: 0.7481 (mtp) REVERT: C 473 PHE cc_start: 0.7717 (m-10) cc_final: 0.6986 (t80) REVERT: D 144 MET cc_start: 0.6649 (mtt) cc_final: 0.6332 (mtp) REVERT: D 277 TYR cc_start: 0.7499 (m-10) cc_final: 0.6252 (t80) REVERT: D 309 PRO cc_start: 0.8181 (Cg_exo) cc_final: 0.7402 (Cg_endo) REVERT: D 410 LEU cc_start: 0.8580 (mm) cc_final: 0.8258 (mm) REVERT: E 239 LEU cc_start: 0.8737 (tp) cc_final: 0.8484 (tp) REVERT: E 269 ILE cc_start: 0.8887 (mm) cc_final: 0.8683 (mm) REVERT: E 310 ARG cc_start: 0.6103 (mtt180) cc_final: 0.5886 (mtt90) REVERT: E 443 ILE cc_start: 0.7641 (mm) cc_final: 0.7407 (mm) REVERT: E 448 ASP cc_start: 0.7728 (m-30) cc_final: 0.7288 (m-30) REVERT: E 467 PHE cc_start: 0.7418 (m-10) cc_final: 0.6981 (t80) outliers start: 11 outliers final: 3 residues processed: 368 average time/residue: 0.1064 time to fit residues: 62.3128 Evaluate side-chains 200 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 197 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 110 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN A 134 HIS ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 GLN B 105 HIS B 159 GLN B 310 ASN B 429 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 276 GLN C 445 ASN C 451 GLN E 262 GLN E 300 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.117040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.092520 restraints weight = 32919.018| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.95 r_work: 0.3145 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17095 Z= 0.146 Angle : 0.584 9.718 23396 Z= 0.292 Chirality : 0.044 0.301 2806 Planarity : 0.004 0.044 2829 Dihedral : 4.690 35.516 2136 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.34 % Allowed : 10.07 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.19), residues: 1970 helix: 2.21 (0.19), residues: 749 sheet: -0.56 (0.25), residues: 394 loop : -0.74 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 455 TYR 0.011 0.001 TYR E 117 PHE 0.024 0.001 PHE C 478 TRP 0.011 0.001 TRP B 197 HIS 0.005 0.001 HIS A 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (17052) covalent geometry : angle 0.57000 / 0.29 (23274) SS BOND : bond 0.00778 / 0.39 ( 7) SS BOND : angle 2.09374 / 1.15 ( 14) hydrogen bonds : bond 0.03973 / 2.72 ( 793) hydrogen bonds : angle 4.39571 / 3.06 ( 2517) link_ALPHA1-3 : bond 0.00590 / 0.33 ( 6) link_ALPHA1-3 : angle 2.61135 / 2.16 ( 18) link_ALPHA1-6 : bond 0.00549 / 0.37 ( 9) link_ALPHA1-6 : angle 1.51419 / 1.02 ( 27) link_BETA1-4 : bond 0.00461 / 0.32 ( 13) link_BETA1-4 : angle 1.70210 / 1.15 ( 39) link_NAG-ASN : bond 0.00148 / 0.09 ( 8) link_NAG-ASN : angle 1.59883 / 0.92 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8896 (m-40) cc_final: 0.8527 (m110) REVERT: A 238 ASP cc_start: 0.8228 (t0) cc_final: 0.7931 (t0) REVERT: A 241 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6945 (mt-10) REVERT: A 252 SER cc_start: 0.9101 (m) cc_final: 0.8826 (p) REVERT: A 324 MET cc_start: 0.7925 (tmm) cc_final: 0.6471 (pmm) REVERT: B 94 ASN cc_start: 0.8648 (t0) cc_final: 0.7265 (t0) REVERT: B 250 SER cc_start: 0.9187 (t) cc_final: 0.8856 (m) REVERT: C 257 MET cc_start: 0.7671 (mmm) cc_final: 0.7171 (tpp) REVERT: C 445 ASN cc_start: 0.7252 (OUTLIER) cc_final: 0.6664 (t0) REVERT: C 473 PHE cc_start: 0.7695 (m-10) cc_final: 0.6838 (t80) REVERT: D 144 MET cc_start: 0.7261 (mtt) cc_final: 0.6876 (mmt) REVERT: D 145 LYS cc_start: 0.8594 (tttt) cc_final: 0.8379 (tttp) REVERT: D 277 TYR cc_start: 0.7741 (m-10) cc_final: 0.6267 (t80) REVERT: D 309 PRO cc_start: 0.7212 (Cg_exo) cc_final: 0.6939 (Cg_endo) REVERT: D 410 LEU cc_start: 0.8454 (mm) cc_final: 0.8160 (mm) REVERT: E 239 LEU cc_start: 0.8646 (tp) cc_final: 0.8368 (tp) outliers start: 43 outliers final: 21 residues processed: 238 average time/residue: 0.1026 time to fit residues: 40.3238 Evaluate side-chains 214 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 296 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 142 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 98 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.5244 > 50:) overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 48 GLN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN C 187 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 305 ASN C 451 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.109562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.085251 restraints weight = 33339.299| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.87 r_work: 0.3018 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17095 Z= 0.213 Angle : 0.621 8.116 23396 Z= 0.311 Chirality : 0.045 0.292 2806 Planarity : 0.004 0.053 2829 Dihedral : 4.919 47.830 2134 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.72 % Allowed : 11.05 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 1970 helix: 1.99 (0.19), residues: 761 sheet: -0.79 (0.24), residues: 416 loop : -0.79 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 79 TYR 0.013 0.001 TYR E 15 PHE 0.016 0.002 PHE B 293 TRP 0.010 0.001 TRP D 311 HIS 0.004 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (17052) covalent geometry : angle 0.60689 / 0.31 (23274) SS BOND : bond 0.00769 / 0.39 ( 7) SS BOND : angle 2.29837 / 1.32 ( 14) hydrogen bonds : bond 0.04299 / 2.94 ( 793) hydrogen bonds : angle 4.42518 / 3.09 ( 2517) link_ALPHA1-3 : bond 0.00442 / 0.25 ( 6) link_ALPHA1-3 : angle 2.36851 / 1.93 ( 18) link_ALPHA1-6 : bond 0.00365 / 0.24 ( 9) link_ALPHA1-6 : angle 1.53700 / 1.03 ( 27) link_BETA1-4 : bond 0.00453 / 0.30 ( 13) link_BETA1-4 : angle 1.80119 / 1.22 ( 39) link_NAG-ASN : bond 0.00234 / 0.12 ( 8) link_NAG-ASN : angle 1.79276 / 1.07 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8920 (m-40) cc_final: 0.8543 (m110) REVERT: A 238 ASP cc_start: 0.8400 (t0) cc_final: 0.8127 (t0) REVERT: A 241 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6934 (mt-10) REVERT: A 252 SER cc_start: 0.9174 (m) cc_final: 0.8953 (p) REVERT: A 308 MET cc_start: 0.8194 (ttp) cc_final: 0.7915 (ttp) REVERT: B 94 ASN cc_start: 0.8892 (t0) cc_final: 0.7704 (t0) REVERT: B 250 SER cc_start: 0.9143 (t) cc_final: 0.8906 (m) REVERT: B 285 MET cc_start: 0.7792 (mmm) cc_final: 0.6618 (tmm) REVERT: B 462 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8985 (m) REVERT: C 255 GLU cc_start: 0.7951 (tp30) cc_final: 0.7315 (tp30) REVERT: C 340 MET cc_start: 0.5749 (mmm) cc_final: 0.5339 (mmm) REVERT: C 499 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7177 (mtm180) REVERT: D 108 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8769 (pt) REVERT: D 144 MET cc_start: 0.7522 (mtt) cc_final: 0.7281 (mtp) REVERT: D 231 LEU cc_start: 0.7864 (mt) cc_final: 0.7580 (mp) REVERT: D 277 TYR cc_start: 0.7752 (m-10) cc_final: 0.6191 (t80) REVERT: D 410 LEU cc_start: 0.8590 (mm) cc_final: 0.8290 (mm) REVERT: E 203 ASP cc_start: 0.7965 (m-30) cc_final: 0.6902 (t70) REVERT: E 239 LEU cc_start: 0.8646 (tp) cc_final: 0.8401 (tp) REVERT: E 310 ARG cc_start: 0.6160 (mtt90) cc_final: 0.5590 (mtt90) outliers start: 50 outliers final: 34 residues processed: 229 average time/residue: 0.1030 time to fit residues: 38.7764 Evaluate side-chains 215 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 458 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 57 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 188 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 451 GLN E 262 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.109453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.084420 restraints weight = 33008.520| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.94 r_work: 0.3008 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17095 Z= 0.179 Angle : 0.576 8.459 23396 Z= 0.286 Chirality : 0.044 0.298 2806 Planarity : 0.004 0.042 2829 Dihedral : 4.802 50.683 2134 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.67 % Allowed : 12.68 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 1970 helix: 2.01 (0.19), residues: 762 sheet: -0.78 (0.25), residues: 412 loop : -0.79 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 79 TYR 0.012 0.001 TYR E 117 PHE 0.024 0.001 PHE C 478 TRP 0.011 0.001 TRP A 187 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (17052) covalent geometry : angle 0.56193 / 0.28 (23274) SS BOND : bond 0.00742 / 0.38 ( 7) SS BOND : angle 2.20365 / 1.24 ( 14) hydrogen bonds : bond 0.03920 / 2.67 ( 793) hydrogen bonds : angle 4.31464 / 3.02 ( 2517) link_ALPHA1-3 : bond 0.00476 / 0.27 ( 6) link_ALPHA1-3 : angle 2.30781 / 1.88 ( 18) link_ALPHA1-6 : bond 0.00419 / 0.27 ( 9) link_ALPHA1-6 : angle 1.49784 / 1.00 ( 27) link_BETA1-4 : bond 0.00464 / 0.32 ( 13) link_BETA1-4 : angle 1.66998 / 1.13 ( 39) link_NAG-ASN : bond 0.00167 / 0.08 ( 8) link_NAG-ASN : angle 1.78431 / 1.08 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 197 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8854 (m-40) cc_final: 0.8486 (m110) REVERT: A 238 ASP cc_start: 0.8467 (t0) cc_final: 0.8184 (t0) REVERT: A 241 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6847 (mt-10) REVERT: A 252 SER cc_start: 0.9170 (m) cc_final: 0.8948 (p) REVERT: A 280 PHE cc_start: 0.7736 (t80) cc_final: 0.6696 (m-10) REVERT: A 324 MET cc_start: 0.7791 (tmm) cc_final: 0.6754 (pmm) REVERT: B 94 ASN cc_start: 0.8752 (t0) cc_final: 0.7518 (t0) REVERT: B 247 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7669 (mt-10) REVERT: B 250 SER cc_start: 0.9189 (t) cc_final: 0.8958 (m) REVERT: B 285 MET cc_start: 0.7811 (mmm) cc_final: 0.6787 (tmm) REVERT: B 314 MET cc_start: 0.7448 (tpp) cc_final: 0.7228 (tpp) REVERT: C 256 LYS cc_start: 0.8622 (tttp) cc_final: 0.8365 (tttm) REVERT: C 257 MET cc_start: 0.7319 (tpp) cc_final: 0.6781 (mmm) REVERT: C 296 MET cc_start: 0.7802 (mtp) cc_final: 0.7562 (mtp) REVERT: C 340 MET cc_start: 0.5760 (mmm) cc_final: 0.5245 (mmm) REVERT: C 499 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7165 (mtm180) REVERT: D 144 MET cc_start: 0.7631 (mtt) cc_final: 0.7328 (mtp) REVERT: D 241 GLU cc_start: 0.6297 (mt-10) cc_final: 0.6012 (mt-10) REVERT: D 277 TYR cc_start: 0.7536 (m-10) cc_final: 0.6103 (t80) REVERT: D 410 LEU cc_start: 0.8645 (mm) cc_final: 0.8389 (mm) REVERT: E 234 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8500 (p) REVERT: E 239 LEU cc_start: 0.8679 (tp) cc_final: 0.8445 (tp) REVERT: E 310 ARG cc_start: 0.6213 (mtt90) cc_final: 0.5783 (mtt90) outliers start: 49 outliers final: 35 residues processed: 228 average time/residue: 0.1020 time to fit residues: 38.4172 Evaluate side-chains 222 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 27 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 139 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.108937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.084459 restraints weight = 32860.638| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.87 r_work: 0.3008 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17095 Z= 0.158 Angle : 0.555 7.942 23396 Z= 0.275 Chirality : 0.043 0.293 2806 Planarity : 0.004 0.042 2829 Dihedral : 4.742 56.324 2133 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.83 % Allowed : 12.85 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 1970 helix: 2.02 (0.19), residues: 768 sheet: -0.85 (0.25), residues: 407 loop : -0.73 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 79 TYR 0.010 0.001 TYR E 117 PHE 0.019 0.001 PHE C 471 TRP 0.010 0.001 TRP A 187 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (17052) covalent geometry : angle 0.54118 / 0.27 (23274) SS BOND : bond 0.00741 / 0.38 ( 7) SS BOND : angle 2.14310 / 1.20 ( 14) hydrogen bonds : bond 0.03775 / 2.57 ( 793) hydrogen bonds : angle 4.23358 / 2.97 ( 2517) link_ALPHA1-3 : bond 0.00473 / 0.27 ( 6) link_ALPHA1-3 : angle 2.25202 / 1.83 ( 18) link_ALPHA1-6 : bond 0.00408 / 0.26 ( 9) link_ALPHA1-6 : angle 1.49731 / 1.00 ( 27) link_BETA1-4 : bond 0.00452 / 0.31 ( 13) link_BETA1-4 : angle 1.65024 / 1.12 ( 39) link_NAG-ASN : bond 0.00151 / 0.08 ( 8) link_NAG-ASN : angle 1.73512 / 1.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8890 (m-40) cc_final: 0.8508 (m110) REVERT: A 238 ASP cc_start: 0.8528 (t0) cc_final: 0.8222 (t0) REVERT: A 241 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6804 (mt-10) REVERT: A 252 SER cc_start: 0.9144 (m) cc_final: 0.8931 (p) REVERT: A 280 PHE cc_start: 0.7740 (t80) cc_final: 0.6670 (m-10) REVERT: A 324 MET cc_start: 0.7726 (tmm) cc_final: 0.6764 (pmm) REVERT: A 400 LYS cc_start: 0.8500 (mttt) cc_final: 0.7901 (mtmm) REVERT: B 94 ASN cc_start: 0.8654 (t0) cc_final: 0.7415 (t0) REVERT: B 247 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7741 (mt-10) REVERT: B 250 SER cc_start: 0.9179 (t) cc_final: 0.8949 (m) REVERT: B 285 MET cc_start: 0.7762 (mmm) cc_final: 0.6778 (tmm) REVERT: C 249 LEU cc_start: 0.7753 (mp) cc_final: 0.7514 (mp) REVERT: C 256 LYS cc_start: 0.8788 (tttp) cc_final: 0.8586 (tttm) REVERT: C 296 MET cc_start: 0.7566 (mtp) cc_final: 0.7284 (mtp) REVERT: C 340 MET cc_start: 0.5792 (mmm) cc_final: 0.5341 (mmm) REVERT: C 499 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7166 (mtm180) REVERT: D 277 TYR cc_start: 0.7654 (m-10) cc_final: 0.6111 (t80) REVERT: D 410 LEU cc_start: 0.8726 (mm) cc_final: 0.8430 (mm) REVERT: E 234 SER cc_start: 0.9011 (t) cc_final: 0.8416 (p) REVERT: E 239 LEU cc_start: 0.8657 (tp) cc_final: 0.8440 (tp) REVERT: E 310 ARG cc_start: 0.6260 (mtt90) cc_final: 0.5789 (mtt180) outliers start: 52 outliers final: 38 residues processed: 224 average time/residue: 0.0988 time to fit residues: 36.6435 Evaluate side-chains 218 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 152 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 189 optimal weight: 30.0000 chunk 172 optimal weight: 0.3980 chunk 71 optimal weight: 10.0000 chunk 163 optimal weight: 0.0870 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.108859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.084357 restraints weight = 32849.556| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.87 r_work: 0.3007 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17095 Z= 0.157 Angle : 0.555 7.873 23396 Z= 0.275 Chirality : 0.043 0.291 2806 Planarity : 0.004 0.041 2829 Dihedral : 4.721 56.975 2133 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.61 % Allowed : 13.34 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 1970 helix: 2.03 (0.19), residues: 768 sheet: -0.78 (0.25), residues: 394 loop : -0.81 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 79 TYR 0.010 0.001 TYR E 117 PHE 0.021 0.001 PHE C 471 TRP 0.012 0.001 TRP A 311 HIS 0.003 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (17052) covalent geometry : angle 0.54126 / 0.27 (23274) SS BOND : bond 0.00733 / 0.36 ( 7) SS BOND : angle 2.14796 / 1.20 ( 14) hydrogen bonds : bond 0.03706 / 2.52 ( 793) hydrogen bonds : angle 4.21257 / 2.96 ( 2517) link_ALPHA1-3 : bond 0.00460 / 0.26 ( 6) link_ALPHA1-3 : angle 2.23779 / 1.81 ( 18) link_ALPHA1-6 : bond 0.00406 / 0.26 ( 9) link_ALPHA1-6 : angle 1.49199 / 1.00 ( 27) link_BETA1-4 : bond 0.00435 / 0.29 ( 13) link_BETA1-4 : angle 1.62134 / 1.10 ( 39) link_NAG-ASN : bond 0.00139 / 0.07 ( 8) link_NAG-ASN : angle 1.70550 / 1.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8899 (m-40) cc_final: 0.8525 (m110) REVERT: A 238 ASP cc_start: 0.8554 (t0) cc_final: 0.8234 (t0) REVERT: A 241 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6776 (mt-10) REVERT: A 252 SER cc_start: 0.9174 (m) cc_final: 0.8961 (p) REVERT: A 280 PHE cc_start: 0.7730 (t80) cc_final: 0.6697 (m-10) REVERT: A 400 LYS cc_start: 0.8505 (mttt) cc_final: 0.7906 (mtmm) REVERT: B 94 ASN cc_start: 0.8659 (t0) cc_final: 0.7431 (t0) REVERT: B 247 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7824 (mt-10) REVERT: B 250 SER cc_start: 0.9219 (t) cc_final: 0.9000 (m) REVERT: B 285 MET cc_start: 0.7815 (mmm) cc_final: 0.6856 (tmm) REVERT: C 249 LEU cc_start: 0.7722 (mp) cc_final: 0.7395 (mp) REVERT: C 296 MET cc_start: 0.7642 (mtp) cc_final: 0.7342 (mtp) REVERT: C 340 MET cc_start: 0.5590 (mmm) cc_final: 0.5186 (mmm) REVERT: C 499 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7195 (mtm180) REVERT: D 277 TYR cc_start: 0.7589 (m-10) cc_final: 0.6075 (t80) REVERT: D 410 LEU cc_start: 0.8782 (mm) cc_final: 0.8489 (mm) REVERT: E 234 SER cc_start: 0.9038 (t) cc_final: 0.8423 (p) REVERT: E 239 LEU cc_start: 0.8670 (tp) cc_final: 0.8436 (tp) REVERT: E 310 ARG cc_start: 0.6463 (mtt90) cc_final: 0.5979 (mtt180) outliers start: 48 outliers final: 39 residues processed: 223 average time/residue: 0.1031 time to fit residues: 37.9066 Evaluate side-chains 224 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 131 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.106881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.082121 restraints weight = 33130.984| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.87 r_work: 0.2970 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17095 Z= 0.221 Angle : 0.617 10.894 23396 Z= 0.303 Chirality : 0.045 0.288 2806 Planarity : 0.004 0.053 2829 Dihedral : 4.850 49.609 2133 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.10 % Allowed : 13.77 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 1970 helix: 1.94 (0.19), residues: 769 sheet: -0.92 (0.25), residues: 396 loop : -0.84 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 79 TYR 0.013 0.001 TYR E 15 PHE 0.014 0.002 PHE D 256 TRP 0.010 0.001 TRP A 187 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (17052) covalent geometry : angle 0.60342 / 0.30 (23274) SS BOND : bond 0.00748 / 0.38 ( 7) SS BOND : angle 2.39863 / 1.37 ( 14) hydrogen bonds : bond 0.03959 / 2.71 ( 793) hydrogen bonds : angle 4.32725 / 3.04 ( 2517) link_ALPHA1-3 : bond 0.00428 / 0.24 ( 6) link_ALPHA1-3 : angle 2.27229 / 1.83 ( 18) link_ALPHA1-6 : bond 0.00362 / 0.22 ( 9) link_ALPHA1-6 : angle 1.53590 / 1.03 ( 27) link_BETA1-4 : bond 0.00455 / 0.31 ( 13) link_BETA1-4 : angle 1.75149 / 1.18 ( 39) link_NAG-ASN : bond 0.00247 / 0.14 ( 8) link_NAG-ASN : angle 1.82520 / 1.11 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8849 (m-40) cc_final: 0.8488 (m110) REVERT: A 238 ASP cc_start: 0.8552 (t0) cc_final: 0.8208 (t0) REVERT: A 241 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6802 (mt-10) REVERT: A 257 LEU cc_start: 0.8616 (tt) cc_final: 0.8395 (tt) REVERT: A 280 PHE cc_start: 0.7711 (t80) cc_final: 0.6652 (m-10) REVERT: A 324 MET cc_start: 0.7849 (tmm) cc_final: 0.6646 (pmm) REVERT: A 433 LEU cc_start: 0.4558 (OUTLIER) cc_final: 0.3828 (mp) REVERT: B 94 ASN cc_start: 0.8709 (t0) cc_final: 0.7506 (t0) REVERT: B 250 SER cc_start: 0.9201 (t) cc_final: 0.8942 (m) REVERT: B 285 MET cc_start: 0.7859 (mmm) cc_final: 0.6896 (tmm) REVERT: C 163 MET cc_start: 0.8655 (ttp) cc_final: 0.8433 (ttm) REVERT: C 340 MET cc_start: 0.5458 (mmm) cc_final: 0.5016 (mmm) REVERT: C 499 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7245 (mtm180) REVERT: D 410 LEU cc_start: 0.8836 (mm) cc_final: 0.8524 (mm) REVERT: E 239 LEU cc_start: 0.8694 (tp) cc_final: 0.8476 (tp) REVERT: E 310 ARG cc_start: 0.6322 (mtt90) cc_final: 0.5795 (mtt180) outliers start: 57 outliers final: 42 residues processed: 221 average time/residue: 0.1015 time to fit residues: 37.0821 Evaluate side-chains 215 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 113 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 114 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 188 optimal weight: 6.9990 chunk 91 optimal weight: 0.0570 chunk 48 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 152 optimal weight: 0.0270 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN E 154 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.109933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.085807 restraints weight = 32897.130| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.86 r_work: 0.3031 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 17095 Z= 0.110 Angle : 0.542 9.017 23396 Z= 0.267 Chirality : 0.042 0.292 2806 Planarity : 0.004 0.051 2829 Dihedral : 4.550 41.148 2133 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.18 % Allowed : 15.13 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1970 helix: 2.13 (0.19), residues: 764 sheet: -0.83 (0.25), residues: 401 loop : -0.77 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.013 0.001 TYR E 117 PHE 0.030 0.001 PHE C 478 TRP 0.012 0.001 TRP A 187 HIS 0.004 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (17052) covalent geometry : angle 0.52864 / 0.26 (23274) SS BOND : bond 0.00725 / 0.36 ( 7) SS BOND : angle 1.99342 / 1.09 ( 14) hydrogen bonds : bond 0.03504 / 2.39 ( 793) hydrogen bonds : angle 4.10441 / 2.89 ( 2517) link_ALPHA1-3 : bond 0.00508 / 0.29 ( 6) link_ALPHA1-3 : angle 2.19910 / 1.78 ( 18) link_ALPHA1-6 : bond 0.00478 / 0.31 ( 9) link_ALPHA1-6 : angle 1.42956 / 0.96 ( 27) link_BETA1-4 : bond 0.00460 / 0.30 ( 13) link_BETA1-4 : angle 1.55609 / 1.07 ( 39) link_NAG-ASN : bond 0.00112 / 0.06 ( 8) link_NAG-ASN : angle 1.64805 / 0.96 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8923 (m-40) cc_final: 0.8537 (m110) REVERT: A 238 ASP cc_start: 0.8494 (t0) cc_final: 0.8181 (t0) REVERT: A 241 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6550 (mt-10) REVERT: A 280 PHE cc_start: 0.7589 (t80) cc_final: 0.6520 (m-10) REVERT: A 313 ARG cc_start: 0.8213 (tpp80) cc_final: 0.7942 (tpp80) REVERT: A 324 MET cc_start: 0.7806 (tmm) cc_final: 0.6610 (pmm) REVERT: A 400 LYS cc_start: 0.8460 (mttt) cc_final: 0.7866 (mtmm) REVERT: A 433 LEU cc_start: 0.4499 (OUTLIER) cc_final: 0.3702 (mt) REVERT: B 94 ASN cc_start: 0.8388 (t0) cc_final: 0.7045 (t0) REVERT: B 250 SER cc_start: 0.9225 (t) cc_final: 0.9016 (m) REVERT: B 285 MET cc_start: 0.7771 (mmm) cc_final: 0.6808 (tmm) REVERT: C 340 MET cc_start: 0.5454 (mmm) cc_final: 0.5211 (mmm) REVERT: C 499 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7202 (mtt180) REVERT: D 228 LEU cc_start: 0.8797 (mt) cc_final: 0.8529 (mt) REVERT: D 410 LEU cc_start: 0.8771 (mm) cc_final: 0.8497 (mm) REVERT: E 234 SER cc_start: 0.8946 (t) cc_final: 0.8263 (p) REVERT: E 239 LEU cc_start: 0.8652 (tp) cc_final: 0.8438 (tp) REVERT: E 246 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7325 (pp30) REVERT: E 275 GLU cc_start: 0.8123 (mp0) cc_final: 0.7840 (mp0) REVERT: E 310 ARG cc_start: 0.6407 (mtt90) cc_final: 0.5814 (mtt90) outliers start: 40 outliers final: 29 residues processed: 220 average time/residue: 0.1015 time to fit residues: 36.9822 Evaluate side-chains 213 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 188 optimal weight: 5.9990 chunk 112 optimal weight: 0.0570 chunk 46 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 overall best weight: 1.3100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 231 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 = 0.3533 r_free = 0.3533 target = 0.109172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.084504 restraints weight = 33126.126| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.90 r_work: 0.3012 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17095 Z= 0.143 Angle : 0.562 8.776 23396 Z= 0.276 Chirality : 0.043 0.289 2806 Planarity : 0.004 0.047 2829 Dihedral : 4.538 39.502 2133 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.45 % Allowed : 15.46 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1970 helix: 2.11 (0.19), residues: 769 sheet: -0.81 (0.25), residues: 402 loop : -0.77 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.010 0.001 TYR E 117 PHE 0.023 0.001 PHE A 284 TRP 0.011 0.001 TRP A 187 HIS 0.004 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (17052) covalent geometry : angle 0.54901 / 0.27 (23274) SS BOND : bond 0.00746 / 0.38 ( 7) SS BOND : angle 2.07837 / 1.15 ( 14) hydrogen bonds : bond 0.03573 / 2.43 ( 793) hydrogen bonds : angle 4.12088 / 2.90 ( 2517) link_ALPHA1-3 : bond 0.00467 / 0.27 ( 6) link_ALPHA1-3 : angle 2.21277 / 1.79 ( 18) link_ALPHA1-6 : bond 0.00412 / 0.26 ( 9) link_ALPHA1-6 : angle 1.48876 / 1.00 ( 27) link_BETA1-4 : bond 0.00433 / 0.29 ( 13) link_BETA1-4 : angle 1.58995 / 1.08 ( 39) link_NAG-ASN : bond 0.00141 / 0.08 ( 8) link_NAG-ASN : angle 1.54789 / 0.92 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8949 (m-40) cc_final: 0.8549 (m110) REVERT: A 238 ASP cc_start: 0.8519 (t0) cc_final: 0.8172 (t0) REVERT: A 241 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6639 (mt-10) REVERT: A 280 PHE cc_start: 0.7583 (t80) cc_final: 0.6554 (m-10) REVERT: A 324 MET cc_start: 0.7768 (tmm) cc_final: 0.6614 (pmm) REVERT: A 400 LYS cc_start: 0.8493 (mttt) cc_final: 0.7884 (mtmm) REVERT: A 433 LEU cc_start: 0.4562 (OUTLIER) cc_final: 0.3775 (mt) REVERT: B 94 ASN cc_start: 0.8435 (t0) cc_final: 0.7076 (t0) REVERT: B 250 SER cc_start: 0.9236 (t) cc_final: 0.9007 (m) REVERT: B 285 MET cc_start: 0.7846 (mmm) cc_final: 0.6845 (tmm) REVERT: C 340 MET cc_start: 0.5470 (mmm) cc_final: 0.5226 (mmm) REVERT: C 499 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7173 (mtt180) REVERT: D 410 LEU cc_start: 0.8762 (mm) cc_final: 0.8484 (mm) REVERT: E 234 SER cc_start: 0.9021 (t) cc_final: 0.8412 (p) REVERT: E 239 LEU cc_start: 0.8676 (tp) cc_final: 0.8453 (tp) REVERT: E 246 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7412 (pp30) REVERT: E 275 GLU cc_start: 0.8211 (mp0) cc_final: 0.7940 (mp0) REVERT: E 310 ARG cc_start: 0.6300 (mtt90) cc_final: 0.5834 (mtt180) outliers start: 45 outliers final: 36 residues processed: 213 average time/residue: 0.1029 time to fit residues: 35.9697 Evaluate side-chains 218 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 150 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 167 optimal weight: 0.3980 chunk 144 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 231 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 = 0.3549 r_free = 0.3549 target = 0.110211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.085571 restraints weight = 32915.371| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.88 r_work: 0.3033 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17095 Z= 0.120 Angle : 0.553 8.674 23396 Z= 0.272 Chirality : 0.043 0.290 2806 Planarity : 0.004 0.047 2829 Dihedral : 4.517 37.840 2133 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.18 % Allowed : 15.57 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.19), residues: 1970 helix: 2.17 (0.19), residues: 763 sheet: -0.88 (0.25), residues: 412 loop : -0.69 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 79 TYR 0.011 0.001 TYR E 117 PHE 0.031 0.001 PHE C 478 TRP 0.011 0.001 TRP A 399 HIS 0.004 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (17052) covalent geometry : angle 0.54019 / 0.27 (23274) SS BOND : bond 0.00719 / 0.36 ( 7) SS BOND : angle 2.03473 / 1.12 ( 14) hydrogen bonds : bond 0.03470 / 2.35 ( 793) hydrogen bonds : angle 4.07856 / 2.88 ( 2517) link_ALPHA1-3 : bond 0.00482 / 0.27 ( 6) link_ALPHA1-3 : angle 2.19601 / 1.78 ( 18) link_ALPHA1-6 : bond 0.00453 / 0.29 ( 9) link_ALPHA1-6 : angle 1.46203 / 0.98 ( 27) link_BETA1-4 : bond 0.00447 / 0.29 ( 13) link_BETA1-4 : angle 1.53803 / 1.05 ( 39) link_NAG-ASN : bond 0.00112 / 0.06 ( 8) link_NAG-ASN : angle 1.53208 / 0.89 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8935 (m-40) cc_final: 0.8533 (m110) REVERT: A 238 ASP cc_start: 0.8466 (t0) cc_final: 0.8114 (t0) REVERT: A 280 PHE cc_start: 0.7573 (t80) cc_final: 0.6542 (m-10) REVERT: A 324 MET cc_start: 0.7611 (tmm) cc_final: 0.6495 (pmm) REVERT: A 400 LYS cc_start: 0.8459 (mttt) cc_final: 0.7838 (mtmm) REVERT: A 433 LEU cc_start: 0.4547 (OUTLIER) cc_final: 0.3781 (mt) REVERT: B 94 ASN cc_start: 0.8376 (t0) cc_final: 0.7120 (t0) REVERT: B 250 SER cc_start: 0.9249 (t) cc_final: 0.9035 (m) REVERT: B 285 MET cc_start: 0.7841 (mmm) cc_final: 0.6822 (tmm) REVERT: B 426 LYS cc_start: 0.8522 (tppt) cc_final: 0.8287 (tppt) REVERT: C 257 MET cc_start: 0.7007 (tpp) cc_final: 0.6798 (mmm) REVERT: C 340 MET cc_start: 0.5491 (mmm) cc_final: 0.5224 (mmm) REVERT: C 499 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7109 (mtt180) REVERT: D 144 MET cc_start: 0.7750 (mtt) cc_final: 0.7467 (mtp) REVERT: D 410 LEU cc_start: 0.8760 (mm) cc_final: 0.8485 (mm) REVERT: E 234 SER cc_start: 0.9014 (t) cc_final: 0.8320 (p) REVERT: E 239 LEU cc_start: 0.8647 (tp) cc_final: 0.8435 (tp) REVERT: E 246 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7391 (pp30) REVERT: E 275 GLU cc_start: 0.8078 (mp0) cc_final: 0.7837 (mp0) REVERT: E 310 ARG cc_start: 0.6348 (mtt90) cc_final: 0.5883 (mtt180) outliers start: 40 outliers final: 37 residues processed: 213 average time/residue: 0.1036 time to fit residues: 36.4241 Evaluate side-chains 221 residues out of total 1837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 459 PHE Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 499 ARG Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 185 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 127 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 146 optimal weight: 0.0870 chunk 180 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.110228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.086034 restraints weight = 32919.358| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.85 r_work: 0.3037 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17095 Z= 0.121 Angle : 0.551 8.499 23396 Z= 0.271 Chirality : 0.043 0.290 2806 Planarity : 0.004 0.049 2829 Dihedral : 4.477 36.441 2133 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.29 % Allowed : 15.84 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 1970 helix: 2.21 (0.19), residues: 757 sheet: -0.85 (0.25), residues: 412 loop : -0.69 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 79 TYR 0.017 0.001 TYR C 439 PHE 0.022 0.001 PHE C 471 TRP 0.010 0.001 TRP A 187 HIS 0.004 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (17052) covalent geometry : angle 0.53854 / 0.27 (23274) SS BOND : bond 0.00725 / 0.36 ( 7) SS BOND : angle 1.99295 / 1.10 ( 14) hydrogen bonds : bond 0.03435 / 2.33 ( 793) hydrogen bonds : angle 4.06250 / 2.87 ( 2517) link_ALPHA1-3 : bond 0.00491 / 0.28 ( 6) link_ALPHA1-3 : angle 2.19268 / 1.77 ( 18) link_ALPHA1-6 : bond 0.00442 / 0.28 ( 9) link_ALPHA1-6 : angle 1.46179 / 0.98 ( 27) link_BETA1-4 : bond 0.00433 / 0.29 ( 13) link_BETA1-4 : angle 1.52883 / 1.04 ( 39) link_NAG-ASN : bond 0.00107 / 0.06 ( 8) link_NAG-ASN : angle 1.47834 / 0.86 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3437.10 seconds wall clock time: 59 minutes 58.19 seconds (3598.19 seconds total)