Starting phenix.real_space_refine on Tue Sep 15 00:44:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ye8_72846/09_2026/9ye8_72846_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ye8_72846/09_2026/9ye8_72846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ye8_72846/09_2026/9ye8_72846_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ye8_72846/09_2026/9ye8_72846_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ye8_72846/09_2026/9ye8_72846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ye8_72846/09_2026/9ye8_72846.map" } resolution = 2.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 75 5.16 5 C 10798 2.51 5 N 2673 2.21 5 O 3067 1.98 5 H 16389 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33002 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 6393 Classifications: {'peptide': 397} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 376} Chain breaks: 2 Chain: "C" Number of atoms: 6324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 6324 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 371} Chain breaks: 1 Chain: "E" Number of atoms: 6577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6577 Classifications: {'peptide': 405} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 379} Chain breaks: 3 Chain: "D" Number of atoms: 7025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 7025 Classifications: {'peptide': 431} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 400} Chain breaks: 1 Chain: "B" Number of atoms: 6397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 6397 Classifications: {'peptide': 406} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 383} Chain breaks: 1 Chain: "F" 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Chain: "B" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.51, per 1000 atoms: 0.17 Number of scatterers: 33002 At special positions: 0 Unit cell: (99.11, 105.655, 167.365, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 O 3067 8.00 N 2673 7.00 C 10798 6.00 H 16389 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.05 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.05 Simple disulfide: pdb=" SG CYS D 130 " - pdb=" SG CYS D 144 " distance=2.05 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 470 " 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 4 " " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 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 J 2 " - " BMA J 3 " NAG-ASN " NAG B 501 " - " ASN B 66 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN C 141 " " NAG H 1 " - " ASN E 141 " " NAG I 1 " - " ASN D 143 " " NAG J 1 " - " ASN B 141 " Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.0 seconds 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3884 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 19 sheets defined 44.9% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.976A pdb=" N GLY A 73 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.666A pdb=" N LYS A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 218 through 231 removed outlier: 3.971A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' 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 318 removed outlier: 3.529A pdb=" N ASP A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.837A pdb=" N ILE A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 324' Processing helix chain 'A' and resid 370 through 437 removed outlier: 3.813A pdb=" N ALA A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLY A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.020A pdb=" N GLY C 73 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 218 through 230 removed outlier: 3.801A pdb=" N GLY C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'C' and resid 241 through 263 Processing helix chain 'C' and resid 272 through 300 Processing helix chain 'C' and resid 309 through 317 Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 370 through 435 removed outlier: 3.660A pdb=" N GLY C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG C 429 " --> pdb=" O VAL C 425 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C 435 " --> pdb=" O ILE C 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.050A pdb=" N ASP E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 229 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 251 Processing helix chain 'E' and resid 252 through 273 removed outlier: 3.782A pdb=" N ASP E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 311 Processing helix chain 'E' and resid 320 through 329 Processing helix chain 'E' and resid 330 through 335 Processing helix chain 'E' and resid 408 through 470 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 70 through 75 removed outlier: 3.996A pdb=" N GLY D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 232 through 243 removed outlier: 3.724A pdb=" N VAL D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 255 through 276 Processing helix chain 'D' and resid 286 through 314 Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.904A pdb=" N GLU D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 413 Processing helix chain 'D' and resid 414 through 473 Proline residue: D 458 - end of helix removed outlier: 3.512A pdb=" N GLN D 470 " --> pdb=" O TRP D 466 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.571A pdb=" N ARG B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 66 removed outlier: 3.755A pdb=" N ASN B 66 " --> pdb=" O TYR B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 66' Processing helix chain 'B' and resid 68 through 73 removed outlier: 4.090A pdb=" N GLY B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.766A pdb=" N TYR B 179 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 238 through 244 removed outlier: 3.557A pdb=" N TYR B 242 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 272 Processing helix chain 'B' and resid 282 through 310 Processing helix chain 'B' and resid 319 through 328 Processing helix chain 'B' and resid 400 through 459 removed outlier: 4.080A pdb=" N ALA B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.152A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.152A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE A 49 " --> pdb=" O ASN A 42 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN A 42 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU A 40 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL A 61 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU A 30 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.438A pdb=" N THR A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU A 199 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR A 196 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR A 190 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN A 208 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.137A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.137A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 49 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN C 42 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASN C 53 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL C 61 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU C 30 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.073A pdb=" N THR C 148 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU C 199 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N THR C 196 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N THR C 189 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR C 198 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N SER C 187 " --> pdb=" O TYR C 198 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP C 200 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS C 185 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR C 202 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY C 183 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N HIS C 204 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER C 181 " --> pdb=" O HIS C 204 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C 206 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.107A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.107A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS E 53 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU E 40 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N TYR E 55 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA E 38 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASP E 57 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE E 36 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLU E 59 " --> pdb=" O GLY E 34 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLY E 34 " --> pdb=" O GLU E 59 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N THR E 61 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N SER E 32 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N TYR E 63 " --> pdb=" O ARG E 30 " (cutoff:3.500A) removed outlier: 13.426A pdb=" N ARG E 30 " --> pdb=" O TYR E 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 92 removed outlier: 6.824A pdb=" N ILE E 217 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 82 removed outlier: 4.027A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLY D 116 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 79 through 82 removed outlier: 4.027A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLY D 116 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR D 51 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER D 44 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR D 53 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU D 42 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN D 55 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR D 63 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP D 32 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL D 31 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N SER D 161 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL D 33 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 93 through 94 removed outlier: 6.885A pdb=" N ILE D 220 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 93 through 94 Processing sheet with id=AB6, first strand: chain 'D' and resid 164 through 167 Processing sheet with id=AB7, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.653A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.653A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR B 49 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER B 42 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR B 51 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU B 40 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER B 53 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLN B 61 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR B 30 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.024A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 215 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.024A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2784 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: 8.04 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16370 1.03 - 1.23: 91 1.23 - 1.43: 7009 1.43 - 1.62: 9831 1.62 - 1.82: 119 Bond restraints: 33420 Sorted by residual: bond pdb=" NZ LYS E 10 " pdb=" HZ3 LYS E 10 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS C 242 " pdb=" HZ1 LYS C 242 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS D 15 " pdb=" HZ2 LYS D 15 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS D 15 " pdb=" HZ3 LYS D 15 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS D 163 " pdb=" HZ2 LYS D 163 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 33415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.55: 60470 12.55 - 25.09: 1 25.09 - 37.64: 0 37.64 - 50.19: 3 50.19 - 62.73: 3 Bond angle restraints: 60477 Sorted by residual: angle pdb=" CA LEU D 410 " pdb=" N LEU D 410 " pdb=" H LEU D 410 " ideal model delta sigma weight residual 114.00 176.73 -62.73 3.00e+00 1.11e-01 4.37e+02 angle pdb=" CA LEU E 407 " pdb=" N LEU E 407 " pdb=" H LEU E 407 " ideal model delta sigma weight residual 114.00 175.15 -61.15 3.00e+00 1.11e-01 4.15e+02 angle pdb=" CA PHE A 326 " pdb=" N PHE A 326 " pdb=" H PHE A 326 " ideal model delta sigma weight residual 114.00 166.01 -52.01 3.00e+00 1.11e-01 3.01e+02 angle pdb=" CA GLU E 206 " pdb=" N GLU E 206 " pdb=" H GLU E 206 " ideal model delta sigma weight residual 114.00 163.27 -49.27 3.00e+00 1.11e-01 2.70e+02 angle pdb=" CA GLU B 399 " pdb=" N GLU B 399 " pdb=" H GLU B 399 " ideal model delta sigma weight residual 114.00 159.15 -45.15 3.00e+00 1.11e-01 2.26e+02 ... (remaining 60472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 14923 21.24 - 42.47: 799 42.47 - 63.71: 259 63.71 - 84.95: 60 84.95 - 106.19: 25 Dihedral angle restraints: 16066 sinusoidal: 8856 harmonic: 7210 Sorted by residual: dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.48 106.19 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" O4 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C5 BMA I 3 " pdb=" O5 BMA I 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.02 105.73 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.96 105.67 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 16063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2154 0.052 - 0.104: 465 0.104 - 0.155: 129 0.155 - 0.207: 5 0.207 - 0.259: 6 Chirality restraints: 2759 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.83e+01 chirality pdb=" C1 MAN G 5 " pdb=" O6 BMA G 3 " pdb=" C2 MAN G 5 " pdb=" O5 MAN G 5 " both_signs ideal model delta sigma weight residual False 2.40 2.29 0.11 2.00e-02 2.50e+03 2.96e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.04e+01 ... (remaining 2756 not shown) Planarity restraints: 4785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.263 2.00e-02 2.50e+03 2.21e-01 6.08e+02 pdb=" C7 NAG G 1 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.176 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.372 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.174 2.00e-02 2.50e+03 1.44e-01 2.60e+02 pdb=" C7 NAG F 1 " -0.045 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.235 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " -0.145 2.00e-02 2.50e+03 1.20e-01 1.79e+02 pdb=" C7 NAG J 2 " 0.042 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " -0.109 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " 0.191 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " 0.021 2.00e-02 2.50e+03 ... (remaining 4782 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 202 2.02 - 2.67: 45996 2.67 - 3.31: 98529 3.31 - 3.96: 132118 3.96 - 4.60: 201940 Nonbonded interactions: 478785 Sorted by model distance: nonbonded pdb=" HH TYR B 15 " pdb=" H TRP B 86 " model vdw 1.375 2.100 nonbonded pdb=" HZ1 LYS A 145 " pdb=" HH TYR A 190 " model vdw 1.394 2.100 nonbonded pdb=" HH TYR D 17 " pdb=" H TRP D 88 " model vdw 1.399 2.100 nonbonded pdb=" HG1 THR C 229 " pdb="HG22 VAL C 285 " model vdw 1.582 2.270 nonbonded pdb=" HG SER D 105 " pdb=" H ILE D 125 " model vdw 1.634 2.100 ... (remaining 478780 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 324 or resid 369 through 436 or resid 501)) selection = chain 'C' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.210 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.290 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 17058 Z= 0.232 Angle : 0.718 20.208 23312 Z= 0.346 Chirality : 0.047 0.259 2759 Planarity : 0.008 0.221 2878 Dihedral : 16.820 106.186 6480 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.85 % Favored : 98.10 % Rotamer: Outliers : 0.27 % Allowed : 8.14 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.19), residues: 2005 helix: 2.37 (0.17), residues: 779 sheet: -0.55 (0.26), residues: 373 loop : -0.06 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 182 TYR 0.008 0.001 TYR A 93 PHE 0.022 0.001 PHE A 284 TRP 0.011 0.001 TRP C 311 HIS 0.010 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (17031) covalent geometry : angle 0.67505 / 0.34 (23237) SS BOND : bond 0.01446 / 0.76 ( 6) SS BOND : angle 1.85094 / 1.15 ( 12) hydrogen bonds : bond 0.15152 / 10.44 ( 885) hydrogen bonds : angle 6.24579 / 4.44 ( 2784) link_ALPHA1-3 : bond 0.00115 / 0.06 ( 3) link_ALPHA1-3 : angle 1.75691 / 0.97 ( 9) link_ALPHA1-6 : bond 0.00084 / 0.04 ( 2) link_ALPHA1-6 : angle 0.92500 / 0.46 ( 6) link_BETA1-4 : bond 0.00552 / 0.29 ( 10) link_BETA1-4 : angle 2.52835 / 2.06 ( 30) link_NAG-ASN : bond 0.15312 / 8.08 ( 6) link_NAG-ASN : angle 8.08153 / 4.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 291 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7655 (mtmt) REVERT: A 279 LEU cc_start: 0.7919 (tp) cc_final: 0.7307 (mt) REVERT: A 306 HIS cc_start: 0.7093 (m90) cc_final: 0.6168 (m90) REVERT: A 384 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6902 (mp0) REVERT: A 387 LYS cc_start: 0.7661 (mtmm) cc_final: 0.7411 (tttp) REVERT: C 280 PHE cc_start: 0.7634 (m-10) cc_final: 0.7038 (t80) REVERT: C 380 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7761 (mttt) REVERT: C 385 THR cc_start: 0.7459 (m) cc_final: 0.7207 (m) REVERT: C 387 LYS cc_start: 0.7682 (tptm) cc_final: 0.7403 (tttt) REVERT: E 238 LEU cc_start: 0.8421 (mm) cc_final: 0.8090 (tp) REVERT: E 319 MET cc_start: 0.7669 (ttm) cc_final: 0.7407 (ttm) REVERT: E 422 ARG cc_start: 0.7594 (ttp-110) cc_final: 0.7379 (ttp-110) REVERT: E 427 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7619 (mt0) REVERT: D 167 LYS cc_start: 0.7293 (ttpp) cc_final: 0.6778 (ttpt) REVERT: D 301 MET cc_start: 0.8350 (mtp) cc_final: 0.8090 (mtt) REVERT: D 332 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6975 (mp0) REVERT: D 340 MET cc_start: 0.8213 (mtp) cc_final: 0.7888 (mtp) REVERT: D 466 TRP cc_start: 0.8111 (t60) cc_final: 0.7789 (t60) REVERT: B 412 GLU cc_start: 0.7112 (tt0) cc_final: 0.6820 (mm-30) REVERT: B 436 ASN cc_start: 0.6974 (t0) cc_final: 0.6710 (t0) outliers start: 5 outliers final: 6 residues processed: 295 average time/residue: 1.2176 time to fit residues: 406.4424 Evaluate side-chains 213 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 207 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain D residue 1 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.0870 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN C 164 GLN C 186 HIS D 431 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.144667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114688 restraints weight = 52182.843| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.71 r_work: 0.3299 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17058 Z= 0.143 Angle : 0.554 6.209 23312 Z= 0.279 Chirality : 0.044 0.192 2759 Planarity : 0.004 0.042 2878 Dihedral : 9.907 84.886 2611 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.80 % Favored : 98.15 % Rotamer: Outliers : 1.08 % Allowed : 11.27 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.19), residues: 2005 helix: 2.75 (0.17), residues: 782 sheet: -0.35 (0.26), residues: 375 loop : 0.02 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 277 TYR 0.016 0.001 TYR D 434 PHE 0.017 0.001 PHE A 284 TRP 0.007 0.001 TRP C 311 HIS 0.004 0.001 HIS A 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (17031) covalent geometry : angle 0.53717 / 0.28 (23237) SS BOND : bond 0.00433 / 0.23 ( 6) SS BOND : angle 1.24275 / 0.75 ( 12) hydrogen bonds : bond 0.04366 / 2.90 ( 885) hydrogen bonds : angle 4.48421 / 3.19 ( 2784) link_ALPHA1-3 : bond 0.00611 / 0.30 ( 3) link_ALPHA1-3 : angle 2.31532 / 1.28 ( 9) link_ALPHA1-6 : bond 0.00174 / 0.08 ( 2) link_ALPHA1-6 : angle 1.85714 / 1.04 ( 6) link_BETA1-4 : bond 0.00520 / 0.35 ( 10) link_BETA1-4 : angle 2.48171 / 1.85 ( 30) link_NAG-ASN : bond 0.00215 / 0.12 ( 6) link_NAG-ASN : angle 3.03119 / 1.83 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LEU cc_start: 0.7653 (tp) cc_final: 0.7244 (mm) REVERT: A 306 HIS cc_start: 0.7096 (m90) cc_final: 0.6066 (m90) REVERT: A 384 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6699 (mp0) REVERT: A 387 LYS cc_start: 0.7390 (mtmm) cc_final: 0.7081 (tttp) REVERT: A 404 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6740 (tmt) REVERT: C 104 LYS cc_start: 0.8541 (mmmm) cc_final: 0.8064 (mttp) REVERT: C 280 PHE cc_start: 0.7540 (m-10) cc_final: 0.6439 (t80) REVERT: E 24 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7153 (mt-10) REVERT: E 238 LEU cc_start: 0.8216 (mm) cc_final: 0.7828 (tp) REVERT: E 319 MET cc_start: 0.7473 (ttm) cc_final: 0.7195 (ttm) REVERT: E 422 ARG cc_start: 0.7400 (ttp-110) cc_final: 0.7139 (ttp-110) REVERT: E 427 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7538 (mt0) REVERT: D 167 LYS cc_start: 0.7027 (ttpp) cc_final: 0.6292 (ttpt) REVERT: D 230 ILE cc_start: 0.7987 (mm) cc_final: 0.7563 (mt) REVERT: D 301 MET cc_start: 0.8287 (mtp) cc_final: 0.7926 (mtt) REVERT: D 332 GLU cc_start: 0.7646 (mt-10) cc_final: 0.6924 (mp0) REVERT: D 340 MET cc_start: 0.8266 (mtp) cc_final: 0.7867 (mtp) REVERT: D 466 TRP cc_start: 0.7804 (t60) cc_final: 0.7585 (t60) REVERT: B 417 GLN cc_start: 0.6857 (mt0) cc_final: 0.6116 (tp-100) REVERT: B 425 SER cc_start: 0.7577 (m) cc_final: 0.7282 (p) REVERT: B 436 ASN cc_start: 0.7214 (t0) cc_final: 0.6998 (t0) outliers start: 20 outliers final: 7 residues processed: 225 average time/residue: 1.1726 time to fit residues: 300.2330 Evaluate side-chains 214 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 205 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 185 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 157 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 GLN C 164 GLN C 393 ASN E 131 GLN E 196 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.142241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111968 restraints weight = 51837.267| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.70 r_work: 0.3264 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17058 Z= 0.176 Angle : 0.550 5.068 23312 Z= 0.278 Chirality : 0.044 0.224 2759 Planarity : 0.005 0.042 2878 Dihedral : 8.582 83.263 2605 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.04 % Favored : 97.91 % Rotamer: Outliers : 1.24 % Allowed : 11.81 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.18), residues: 2005 helix: 2.73 (0.17), residues: 782 sheet: -0.32 (0.25), residues: 380 loop : -0.07 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 9 TYR 0.015 0.002 TYR D 434 PHE 0.016 0.002 PHE A 284 TRP 0.008 0.001 TRP D 176 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (17031) covalent geometry : angle 0.53660 / 0.28 (23237) SS BOND : bond 0.00419 / 0.22 ( 6) SS BOND : angle 1.34878 / 0.81 ( 12) hydrogen bonds : bond 0.04418 / 2.95 ( 885) hydrogen bonds : angle 4.36204 / 3.10 ( 2784) link_ALPHA1-3 : bond 0.00758 / 0.37 ( 3) link_ALPHA1-3 : angle 1.65111 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00291 / 0.14 ( 2) link_ALPHA1-6 : angle 1.73880 / 0.98 ( 6) link_BETA1-4 : bond 0.00489 / 0.33 ( 10) link_BETA1-4 : angle 2.60651 / 1.95 ( 30) link_NAG-ASN : bond 0.00477 / 0.30 ( 6) link_NAG-ASN : angle 2.25136 / 1.43 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LEU cc_start: 0.7613 (tp) cc_final: 0.6981 (mt) REVERT: A 380 LYS cc_start: 0.7597 (mtpt) cc_final: 0.7328 (mtmt) REVERT: A 384 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6688 (mp0) REVERT: A 387 LYS cc_start: 0.7435 (mtmm) cc_final: 0.7077 (tttp) REVERT: C 104 LYS cc_start: 0.8622 (mmmm) cc_final: 0.8155 (mttp) REVERT: C 280 PHE cc_start: 0.7498 (m-10) cc_final: 0.6479 (t80) REVERT: C 380 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7780 (mppt) REVERT: C 387 LYS cc_start: 0.7283 (tptm) cc_final: 0.6691 (ttmt) REVERT: E 24 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7169 (mt-10) REVERT: E 238 LEU cc_start: 0.8249 (mm) cc_final: 0.7887 (tp) REVERT: E 319 MET cc_start: 0.7464 (ttm) cc_final: 0.7146 (ttm) REVERT: E 422 ARG cc_start: 0.7428 (ttp-110) cc_final: 0.7174 (ttp-110) REVERT: E 427 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7577 (mt0) REVERT: D 9 ARG cc_start: 0.7998 (ttm170) cc_final: 0.7673 (ttm170) REVERT: D 167 LYS cc_start: 0.7050 (ttpp) cc_final: 0.6323 (ttpt) REVERT: D 230 ILE cc_start: 0.8006 (mm) cc_final: 0.7596 (mt) REVERT: D 301 MET cc_start: 0.8326 (mtp) cc_final: 0.7963 (mtt) REVERT: D 332 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: D 340 MET cc_start: 0.8381 (mtp) cc_final: 0.8024 (mtp) REVERT: D 466 TRP cc_start: 0.7888 (t60) cc_final: 0.7660 (t60) REVERT: B 417 GLN cc_start: 0.6915 (mt0) cc_final: 0.6132 (tp-100) REVERT: B 425 SER cc_start: 0.7562 (m) cc_final: 0.7268 (p) outliers start: 23 outliers final: 10 residues processed: 223 average time/residue: 1.2069 time to fit residues: 304.5817 Evaluate side-chains 218 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 205 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 437 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 70 optimal weight: 0.1980 chunk 123 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN C 164 GLN C 217 ASN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.142815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.112594 restraints weight = 51761.512| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.71 r_work: 0.3270 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17058 Z= 0.144 Angle : 0.517 5.258 23312 Z= 0.263 Chirality : 0.043 0.214 2759 Planarity : 0.004 0.038 2878 Dihedral : 7.782 77.851 2605 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.95 % Favored : 98.00 % Rotamer: Outliers : 1.78 % Allowed : 10.95 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.19), residues: 2005 helix: 2.83 (0.17), residues: 785 sheet: -0.30 (0.25), residues: 380 loop : -0.06 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 30 TYR 0.015 0.001 TYR D 434 PHE 0.013 0.001 PHE D 291 TRP 0.007 0.001 TRP C 311 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (17031) covalent geometry : angle 0.50374 / 0.26 (23237) SS BOND : bond 0.00383 / 0.20 ( 6) SS BOND : angle 1.24737 / 0.74 ( 12) hydrogen bonds : bond 0.04055 / 2.70 ( 885) hydrogen bonds : angle 4.20535 / 2.99 ( 2784) link_ALPHA1-3 : bond 0.00853 / 0.41 ( 3) link_ALPHA1-3 : angle 1.84660 / 1.01 ( 9) link_ALPHA1-6 : bond 0.00319 / 0.15 ( 2) link_ALPHA1-6 : angle 1.91952 / 1.08 ( 6) link_BETA1-4 : bond 0.00398 / 0.25 ( 10) link_BETA1-4 : angle 2.31121 / 1.67 ( 30) link_NAG-ASN : bond 0.00289 / 0.14 ( 6) link_NAG-ASN : angle 2.25797 / 1.42 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8505 (mmm) cc_final: 0.8220 (mmm) REVERT: A 279 LEU cc_start: 0.7607 (tp) cc_final: 0.7177 (mm) REVERT: A 380 LYS cc_start: 0.7563 (mtpt) cc_final: 0.7271 (mtmt) REVERT: A 384 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6670 (mp0) REVERT: A 387 LYS cc_start: 0.7437 (mtmm) cc_final: 0.7084 (tttp) REVERT: A 404 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6699 (tmt) REVERT: A 408 HIS cc_start: 0.6915 (m-70) cc_final: 0.6460 (m90) REVERT: C 104 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8173 (mttp) REVERT: C 280 PHE cc_start: 0.7503 (m-10) cc_final: 0.6460 (t80) REVERT: C 380 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7826 (mppt) REVERT: C 385 THR cc_start: 0.7356 (m) cc_final: 0.7069 (m) REVERT: C 387 LYS cc_start: 0.7302 (tptm) cc_final: 0.6694 (ttmt) REVERT: E 24 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7134 (mt-10) REVERT: E 238 LEU cc_start: 0.8238 (mm) cc_final: 0.7878 (tp) REVERT: E 319 MET cc_start: 0.7462 (ttm) cc_final: 0.7114 (ttm) REVERT: E 336 ARG cc_start: 0.7456 (mmt90) cc_final: 0.7236 (mmt90) REVERT: E 422 ARG cc_start: 0.7408 (ttp-110) cc_final: 0.7156 (ttp-110) REVERT: E 427 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7550 (mt0) REVERT: D 167 LYS cc_start: 0.7050 (ttpp) cc_final: 0.6298 (ttpt) REVERT: D 230 ILE cc_start: 0.7966 (mm) cc_final: 0.7580 (mt) REVERT: D 301 MET cc_start: 0.8300 (mtp) cc_final: 0.7935 (mtt) REVERT: D 332 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: D 340 MET cc_start: 0.8387 (mtp) cc_final: 0.8025 (mtp) REVERT: D 466 TRP cc_start: 0.7875 (t60) cc_final: 0.7656 (t60) REVERT: B 76 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8305 (mt-10) REVERT: B 417 GLN cc_start: 0.6920 (mt0) cc_final: 0.6132 (tp-100) REVERT: B 425 SER cc_start: 0.7614 (m) cc_final: 0.7323 (p) outliers start: 33 outliers final: 16 residues processed: 230 average time/residue: 1.1854 time to fit residues: 308.6121 Evaluate side-chains 225 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain B residue 76 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 164 GLN C 299 HIS C 393 ASN B 432 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.140880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110505 restraints weight = 51788.374| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.71 r_work: 0.3241 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17058 Z= 0.211 Angle : 0.566 5.812 23312 Z= 0.290 Chirality : 0.044 0.219 2759 Planarity : 0.005 0.052 2878 Dihedral : 7.972 79.232 2605 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.81 % Rotamer: Outliers : 1.73 % Allowed : 11.00 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.18), residues: 2005 helix: 2.67 (0.17), residues: 784 sheet: -0.40 (0.24), residues: 392 loop : -0.13 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 195 TYR 0.014 0.002 TYR D 434 PHE 0.019 0.002 PHE A 284 TRP 0.010 0.002 TRP D 176 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (17031) covalent geometry : angle 0.55179 / 0.29 (23237) SS BOND : bond 0.00505 / 0.27 ( 6) SS BOND : angle 1.58441 / 0.94 ( 12) hydrogen bonds : bond 0.04409 / 2.94 ( 885) hydrogen bonds : angle 4.32143 / 3.07 ( 2784) link_ALPHA1-3 : bond 0.00782 / 0.38 ( 3) link_ALPHA1-3 : angle 1.68506 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00200 / 0.10 ( 2) link_ALPHA1-6 : angle 2.04289 / 1.16 ( 6) link_BETA1-4 : bond 0.00571 / 0.37 ( 10) link_BETA1-4 : angle 2.59445 / 1.89 ( 30) link_NAG-ASN : bond 0.00589 / 0.29 ( 6) link_NAG-ASN : angle 2.55327 / 1.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LEU cc_start: 0.7602 (tp) cc_final: 0.7155 (mm) REVERT: A 384 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6642 (mp0) REVERT: A 387 LYS cc_start: 0.7446 (mtmm) cc_final: 0.6998 (tttp) REVERT: A 391 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7791 (mt-10) REVERT: C 104 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8110 (mttp) REVERT: C 280 PHE cc_start: 0.7477 (m-10) cc_final: 0.6490 (t80) REVERT: C 385 THR cc_start: 0.7373 (m) cc_final: 0.7092 (m) REVERT: C 387 LYS cc_start: 0.7374 (tptm) cc_final: 0.6705 (ttmt) REVERT: E 24 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: E 238 LEU cc_start: 0.8263 (mm) cc_final: 0.7899 (tp) REVERT: E 319 MET cc_start: 0.7607 (ttm) cc_final: 0.7269 (ttm) REVERT: E 336 ARG cc_start: 0.7415 (mmt90) cc_final: 0.7194 (mmt90) REVERT: E 422 ARG cc_start: 0.7380 (ttp-110) cc_final: 0.7171 (ttp-110) REVERT: E 427 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7561 (mt0) REVERT: D 167 LYS cc_start: 0.7112 (ttpp) cc_final: 0.6428 (ttpt) REVERT: D 230 ILE cc_start: 0.7973 (mm) cc_final: 0.7596 (mt) REVERT: D 301 MET cc_start: 0.8333 (mtp) cc_final: 0.7969 (mtt) REVERT: D 332 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: D 340 MET cc_start: 0.8437 (mtp) cc_final: 0.7983 (mtp) REVERT: D 449 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7374 (m-30) REVERT: D 466 TRP cc_start: 0.7923 (t60) cc_final: 0.7681 (t60) REVERT: B 45 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: B 76 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: B 417 GLN cc_start: 0.6951 (mt0) cc_final: 0.6144 (tp-100) REVERT: B 425 SER cc_start: 0.7585 (m) cc_final: 0.7286 (p) outliers start: 32 outliers final: 15 residues processed: 231 average time/residue: 1.2093 time to fit residues: 317.0358 Evaluate side-chains 227 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 76 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 66 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 41 optimal weight: 0.0370 chunk 161 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN C 164 GLN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.142878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.112864 restraints weight = 51722.730| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.70 r_work: 0.3273 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17058 Z= 0.119 Angle : 0.500 4.721 23312 Z= 0.255 Chirality : 0.042 0.226 2759 Planarity : 0.004 0.041 2878 Dihedral : 7.349 72.285 2605 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.80 % Favored : 98.15 % Rotamer: Outliers : 1.13 % Allowed : 11.87 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.19), residues: 2005 helix: 2.92 (0.18), residues: 783 sheet: -0.31 (0.25), residues: 379 loop : -0.07 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 30 TYR 0.014 0.001 TYR D 434 PHE 0.011 0.001 PHE D 291 TRP 0.008 0.001 TRP D 62 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (17031) covalent geometry : angle 0.48956 / 0.25 (23237) SS BOND : bond 0.00280 / 0.15 ( 6) SS BOND : angle 1.02330 / 0.61 ( 12) hydrogen bonds : bond 0.03894 / 2.59 ( 885) hydrogen bonds : angle 4.10437 / 2.92 ( 2784) link_ALPHA1-3 : bond 0.00802 / 0.39 ( 3) link_ALPHA1-3 : angle 1.75727 / 0.98 ( 9) link_ALPHA1-6 : bond 0.00421 / 0.20 ( 2) link_ALPHA1-6 : angle 1.90887 / 1.08 ( 6) link_BETA1-4 : bond 0.00339 / 0.22 ( 10) link_BETA1-4 : angle 2.06007 / 1.48 ( 30) link_NAG-ASN : bond 0.00208 / 0.11 ( 6) link_NAG-ASN : angle 2.04404 / 1.29 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LEU cc_start: 0.7573 (tp) cc_final: 0.7143 (mm) REVERT: A 384 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6671 (mp0) REVERT: A 387 LYS cc_start: 0.7421 (mtmm) cc_final: 0.7080 (tttp) REVERT: A 408 HIS cc_start: 0.6910 (m-70) cc_final: 0.6706 (m170) REVERT: C 104 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8126 (mttp) REVERT: C 280 PHE cc_start: 0.7481 (m-10) cc_final: 0.6487 (t80) REVERT: C 380 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7733 (mppt) REVERT: C 385 THR cc_start: 0.7366 (m) cc_final: 0.7073 (m) REVERT: C 387 LYS cc_start: 0.7373 (tptm) cc_final: 0.6729 (ttmt) REVERT: E 238 LEU cc_start: 0.8248 (mm) cc_final: 0.7882 (tp) REVERT: E 319 MET cc_start: 0.7634 (ttm) cc_final: 0.7367 (ttm) REVERT: E 336 ARG cc_start: 0.7365 (mmt90) cc_final: 0.7112 (mmt90) REVERT: E 422 ARG cc_start: 0.7375 (ttp-110) cc_final: 0.7163 (ttp-110) REVERT: E 427 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7548 (mt0) REVERT: D 167 LYS cc_start: 0.7093 (ttpp) cc_final: 0.6413 (ttpt) REVERT: D 230 ILE cc_start: 0.7935 (mm) cc_final: 0.7565 (mt) REVERT: D 301 MET cc_start: 0.8335 (mtp) cc_final: 0.7978 (mtt) REVERT: D 332 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: D 340 MET cc_start: 0.8414 (mtp) cc_final: 0.7954 (mtp) REVERT: D 466 TRP cc_start: 0.7869 (t60) cc_final: 0.7652 (t60) REVERT: B 76 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8301 (mt-10) REVERT: B 417 GLN cc_start: 0.6941 (mt0) cc_final: 0.6134 (tp-100) REVERT: B 425 SER cc_start: 0.7614 (m) cc_final: 0.7334 (p) outliers start: 21 outliers final: 11 residues processed: 222 average time/residue: 1.1962 time to fit residues: 302.2481 Evaluate side-chains 219 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain B residue 76 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 115 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 393 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.140811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110482 restraints weight = 52071.087| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.71 r_work: 0.3242 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17058 Z= 0.209 Angle : 0.558 6.056 23312 Z= 0.285 Chirality : 0.044 0.247 2759 Planarity : 0.005 0.049 2878 Dihedral : 7.737 73.599 2605 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.04 % Favored : 97.91 % Rotamer: Outliers : 1.29 % Allowed : 11.92 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.18), residues: 2005 helix: 2.74 (0.18), residues: 784 sheet: -0.38 (0.24), residues: 392 loop : -0.11 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 195 TYR 0.014 0.002 TYR D 434 PHE 0.016 0.002 PHE D 291 TRP 0.010 0.002 TRP D 176 HIS 0.004 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (17031) covalent geometry : angle 0.54313 / 0.28 (23237) SS BOND : bond 0.00512 / 0.27 ( 6) SS BOND : angle 1.57256 / 0.93 ( 12) hydrogen bonds : bond 0.04309 / 2.88 ( 885) hydrogen bonds : angle 4.25729 / 3.02 ( 2784) link_ALPHA1-3 : bond 0.00696 / 0.34 ( 3) link_ALPHA1-3 : angle 1.64024 / 0.97 ( 9) link_ALPHA1-6 : bond 0.00211 / 0.10 ( 2) link_ALPHA1-6 : angle 2.05230 / 1.17 ( 6) link_BETA1-4 : bond 0.00565 / 0.37 ( 10) link_BETA1-4 : angle 2.52763 / 1.84 ( 30) link_NAG-ASN : bond 0.00544 / 0.27 ( 6) link_NAG-ASN : angle 2.58652 / 1.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LEU cc_start: 0.7638 (tp) cc_final: 0.7206 (mm) REVERT: A 384 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6656 (mp0) REVERT: A 387 LYS cc_start: 0.7447 (mtmm) cc_final: 0.7141 (tttp) REVERT: A 408 HIS cc_start: 0.6970 (m-70) cc_final: 0.6712 (m170) REVERT: C 2 GLU cc_start: 0.6678 (tp30) cc_final: 0.5867 (tm-30) REVERT: C 77 LYS cc_start: 0.8499 (ptpt) cc_final: 0.7965 (pttm) REVERT: C 104 LYS cc_start: 0.8619 (mmmm) cc_final: 0.8151 (mttp) REVERT: C 280 PHE cc_start: 0.7446 (m-10) cc_final: 0.6486 (t80) REVERT: C 380 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7881 (mppt) REVERT: C 385 THR cc_start: 0.7350 (m) cc_final: 0.7083 (m) REVERT: E 24 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: E 238 LEU cc_start: 0.8266 (mm) cc_final: 0.7863 (tp) REVERT: E 319 MET cc_start: 0.7612 (ttm) cc_final: 0.7215 (ttm) REVERT: E 336 ARG cc_start: 0.7377 (mmt90) cc_final: 0.7122 (mmt90) REVERT: E 422 ARG cc_start: 0.7418 (ttp-110) cc_final: 0.7188 (ttp-110) REVERT: E 427 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7559 (mt0) REVERT: D 167 LYS cc_start: 0.7135 (ttpp) cc_final: 0.6450 (ttpt) REVERT: D 230 ILE cc_start: 0.7951 (mm) cc_final: 0.7591 (mt) REVERT: D 301 MET cc_start: 0.8323 (mtp) cc_final: 0.7962 (mtt) REVERT: D 332 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: D 340 MET cc_start: 0.8454 (mtp) cc_final: 0.8079 (mtp) REVERT: D 466 TRP cc_start: 0.7921 (t60) cc_final: 0.7680 (t60) REVERT: B 45 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: B 76 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8345 (mt-10) REVERT: B 417 GLN cc_start: 0.6995 (mt0) cc_final: 0.6168 (tp-100) REVERT: B 425 SER cc_start: 0.7626 (m) cc_final: 0.7324 (p) outliers start: 24 outliers final: 14 residues processed: 222 average time/residue: 1.2018 time to fit residues: 302.2153 Evaluate side-chains 225 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 435 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 50 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 183 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN D 431 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.142483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.112453 restraints weight = 51843.000| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.71 r_work: 0.3267 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17058 Z= 0.126 Angle : 0.501 4.742 23312 Z= 0.256 Chirality : 0.042 0.210 2759 Planarity : 0.004 0.044 2878 Dihedral : 7.277 68.133 2605 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.96 % Rotamer: Outliers : 1.13 % Allowed : 12.03 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.19), residues: 2005 helix: 2.93 (0.18), residues: 784 sheet: -0.35 (0.25), residues: 388 loop : -0.04 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 30 TYR 0.013 0.001 TYR D 434 PHE 0.012 0.001 PHE D 291 TRP 0.008 0.001 TRP C 311 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (17031) covalent geometry : angle 0.49081 / 0.25 (23237) SS BOND : bond 0.00286 / 0.15 ( 6) SS BOND : angle 1.05247 / 0.63 ( 12) hydrogen bonds : bond 0.03896 / 2.59 ( 885) hydrogen bonds : angle 4.08473 / 2.91 ( 2784) link_ALPHA1-3 : bond 0.00783 / 0.38 ( 3) link_ALPHA1-3 : angle 1.70167 / 0.97 ( 9) link_ALPHA1-6 : bond 0.00431 / 0.21 ( 2) link_ALPHA1-6 : angle 1.89710 / 1.08 ( 6) link_BETA1-4 : bond 0.00359 / 0.23 ( 10) link_BETA1-4 : angle 2.07733 / 1.49 ( 30) link_NAG-ASN : bond 0.00238 / 0.12 ( 6) link_NAG-ASN : angle 1.96829 / 1.26 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 LEU cc_start: 0.7560 (tp) cc_final: 0.7138 (mm) REVERT: A 384 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6682 (mp0) REVERT: A 387 LYS cc_start: 0.7432 (mtmm) cc_final: 0.7129 (tttp) REVERT: A 408 HIS cc_start: 0.7013 (m-70) cc_final: 0.6728 (m170) REVERT: C 77 LYS cc_start: 0.8468 (ptpt) cc_final: 0.7943 (pttm) REVERT: C 104 LYS cc_start: 0.8516 (mmmm) cc_final: 0.8075 (mttp) REVERT: C 280 PHE cc_start: 0.7482 (m-10) cc_final: 0.6502 (t80) REVERT: C 380 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7761 (mppt) REVERT: C 385 THR cc_start: 0.7366 (m) cc_final: 0.7087 (m) REVERT: E 238 LEU cc_start: 0.8233 (mm) cc_final: 0.7883 (tp) REVERT: E 319 MET cc_start: 0.7666 (ttm) cc_final: 0.7258 (ttm) REVERT: E 336 ARG cc_start: 0.7363 (mmt90) cc_final: 0.7060 (mmt90) REVERT: E 422 ARG cc_start: 0.7402 (ttp-110) cc_final: 0.7188 (ttp-110) REVERT: E 427 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7557 (mt0) REVERT: D 167 LYS cc_start: 0.7102 (ttpp) cc_final: 0.6415 (ttpt) REVERT: D 230 ILE cc_start: 0.7920 (mm) cc_final: 0.7563 (mt) REVERT: D 301 MET cc_start: 0.8347 (mtp) cc_final: 0.7992 (mtt) REVERT: D 332 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: D 340 MET cc_start: 0.8420 (mtp) cc_final: 0.7959 (mtp) REVERT: D 466 TRP cc_start: 0.7886 (t60) cc_final: 0.7666 (t60) REVERT: B 45 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: B 76 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8312 (mt-10) REVERT: B 417 GLN cc_start: 0.6974 (mt0) cc_final: 0.6153 (tp-100) REVERT: B 425 SER cc_start: 0.7610 (m) cc_final: 0.7311 (p) outliers start: 21 outliers final: 13 residues processed: 222 average time/residue: 1.1977 time to fit residues: 301.7223 Evaluate side-chains 223 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 435 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 163 optimal weight: 0.3980 chunk 190 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 160 optimal weight: 0.0270 chunk 10 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 393 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.141338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.111127 restraints weight = 51642.421| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.71 r_work: 0.3250 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17058 Z= 0.180 Angle : 0.539 5.748 23312 Z= 0.275 Chirality : 0.043 0.240 2759 Planarity : 0.005 0.046 2878 Dihedral : 7.450 68.049 2605 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.04 % Favored : 97.91 % Rotamer: Outliers : 1.19 % Allowed : 12.19 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.19), residues: 2005 helix: 2.81 (0.18), residues: 784 sheet: -0.34 (0.25), residues: 391 loop : -0.08 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 195 TYR 0.013 0.002 TYR D 434 PHE 0.017 0.002 PHE A 284 TRP 0.008 0.001 TRP D 176 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (17031) covalent geometry : angle 0.52536 / 0.27 (23237) SS BOND : bond 0.00455 / 0.24 ( 6) SS BOND : angle 1.44864 / 0.86 ( 12) hydrogen bonds : bond 0.04128 / 2.76 ( 885) hydrogen bonds : angle 4.18091 / 2.97 ( 2784) link_ALPHA1-3 : bond 0.00703 / 0.34 ( 3) link_ALPHA1-3 : angle 1.64669 / 0.96 ( 9) link_ALPHA1-6 : bond 0.00315 / 0.15 ( 2) link_ALPHA1-6 : angle 1.94081 / 1.10 ( 6) link_BETA1-4 : bond 0.00489 / 0.32 ( 10) link_BETA1-4 : angle 2.38182 / 1.73 ( 30) link_NAG-ASN : bond 0.00455 / 0.22 ( 6) link_NAG-ASN : angle 2.47837 / 1.55 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LEU cc_start: 0.7621 (tp) cc_final: 0.7206 (mm) REVERT: A 384 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6707 (mp0) REVERT: A 387 LYS cc_start: 0.7459 (mtmm) cc_final: 0.7159 (tttp) REVERT: A 408 HIS cc_start: 0.7052 (m-70) cc_final: 0.6768 (m170) REVERT: C 2 GLU cc_start: 0.6650 (tp30) cc_final: 0.5802 (tm-30) REVERT: C 77 LYS cc_start: 0.8488 (ptpt) cc_final: 0.7958 (pttm) REVERT: C 104 LYS cc_start: 0.8606 (mmmm) cc_final: 0.8070 (mttp) REVERT: C 280 PHE cc_start: 0.7467 (m-10) cc_final: 0.6520 (t80) REVERT: C 380 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7838 (mppt) REVERT: C 385 THR cc_start: 0.7327 (m) cc_final: 0.7064 (m) REVERT: E 238 LEU cc_start: 0.8256 (mm) cc_final: 0.7905 (tp) REVERT: E 319 MET cc_start: 0.7575 (ttm) cc_final: 0.7189 (ttm) REVERT: E 336 ARG cc_start: 0.7366 (mmt90) cc_final: 0.7062 (mmt90) REVERT: E 422 ARG cc_start: 0.7416 (ttp-110) cc_final: 0.7184 (ttp-110) REVERT: E 427 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7484 (mt0) REVERT: D 167 LYS cc_start: 0.7142 (ttpp) cc_final: 0.6452 (ttpt) REVERT: D 230 ILE cc_start: 0.7974 (mm) cc_final: 0.7611 (mt) REVERT: D 301 MET cc_start: 0.8337 (mtp) cc_final: 0.7978 (mtt) REVERT: D 332 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: D 340 MET cc_start: 0.8433 (mtp) cc_final: 0.8041 (mtp) REVERT: D 446 ARG cc_start: 0.7411 (mtp85) cc_final: 0.7203 (mtp85) REVERT: D 449 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: B 45 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: B 417 GLN cc_start: 0.7005 (mt0) cc_final: 0.6165 (tp-100) REVERT: B 425 SER cc_start: 0.7609 (m) cc_final: 0.7299 (p) outliers start: 22 outliers final: 14 residues processed: 221 average time/residue: 1.2058 time to fit residues: 303.3696 Evaluate side-chains 225 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 435 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 110 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 169 optimal weight: 0.2980 chunk 102 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.141910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.111760 restraints weight = 51926.802| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.73 r_work: 0.3258 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17058 Z= 0.153 Angle : 0.522 6.298 23312 Z= 0.267 Chirality : 0.043 0.240 2759 Planarity : 0.004 0.047 2878 Dihedral : 7.182 65.128 2605 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.04 % Favored : 97.91 % Rotamer: Outliers : 1.08 % Allowed : 12.57 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.19), residues: 2005 helix: 2.86 (0.18), residues: 784 sheet: -0.34 (0.25), residues: 389 loop : -0.05 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 195 TYR 0.013 0.001 TYR D 434 PHE 0.013 0.001 PHE D 291 TRP 0.008 0.001 TRP C 311 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (17031) covalent geometry : angle 0.51016 / 0.26 (23237) SS BOND : bond 0.00370 / 0.19 ( 6) SS BOND : angle 1.22880 / 0.73 ( 12) hydrogen bonds : bond 0.04007 / 2.67 ( 885) hydrogen bonds : angle 4.13138 / 2.94 ( 2784) link_ALPHA1-3 : bond 0.00721 / 0.35 ( 3) link_ALPHA1-3 : angle 1.63996 / 0.94 ( 9) link_ALPHA1-6 : bond 0.00374 / 0.18 ( 2) link_ALPHA1-6 : angle 1.89518 / 1.08 ( 6) link_BETA1-4 : bond 0.00408 / 0.27 ( 10) link_BETA1-4 : angle 2.21406 / 1.60 ( 30) link_NAG-ASN : bond 0.00326 / 0.16 ( 6) link_NAG-ASN : angle 2.20102 / 1.38 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LEU cc_start: 0.7559 (tp) cc_final: 0.7142 (mm) REVERT: A 384 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6703 (mp0) REVERT: A 387 LYS cc_start: 0.7454 (mtmm) cc_final: 0.7159 (tttp) REVERT: A 408 HIS cc_start: 0.7042 (m-70) cc_final: 0.6762 (m170) REVERT: C 2 GLU cc_start: 0.6631 (tp30) cc_final: 0.5816 (tm-30) REVERT: C 77 LYS cc_start: 0.8483 (ptpt) cc_final: 0.7952 (pttm) REVERT: C 104 LYS cc_start: 0.8524 (mmmm) cc_final: 0.8085 (mttp) REVERT: C 280 PHE cc_start: 0.7441 (m-10) cc_final: 0.6522 (t80) REVERT: C 380 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7830 (mppt) REVERT: C 385 THR cc_start: 0.7252 (m) cc_final: 0.6993 (m) REVERT: E 238 LEU cc_start: 0.8246 (mm) cc_final: 0.7882 (tp) REVERT: E 319 MET cc_start: 0.7618 (ttm) cc_final: 0.7210 (ttm) REVERT: E 336 ARG cc_start: 0.7377 (mmt90) cc_final: 0.7059 (mmt90) REVERT: E 422 ARG cc_start: 0.7409 (ttp-110) cc_final: 0.7178 (ttp-110) REVERT: E 427 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7482 (mt0) REVERT: D 167 LYS cc_start: 0.7149 (ttpp) cc_final: 0.6464 (ttpt) REVERT: D 230 ILE cc_start: 0.7897 (mm) cc_final: 0.7546 (mt) REVERT: D 301 MET cc_start: 0.8351 (mtp) cc_final: 0.7993 (mtt) REVERT: D 332 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: D 340 MET cc_start: 0.8434 (mtp) cc_final: 0.7960 (mtp) REVERT: B 45 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: B 417 GLN cc_start: 0.7005 (mt0) cc_final: 0.6377 (tp-100) REVERT: B 425 SER cc_start: 0.7605 (m) cc_final: 0.7297 (p) outliers start: 20 outliers final: 12 residues processed: 220 average time/residue: 1.2125 time to fit residues: 302.4517 Evaluate side-chains 217 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 435 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 35 optimal weight: 3.9990 chunk 80 optimal weight: 0.0050 chunk 161 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 393 ASN D 431 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.141625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.111452 restraints weight = 52062.471| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.71 r_work: 0.3254 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17058 Z= 0.167 Angle : 0.531 5.992 23312 Z= 0.271 Chirality : 0.043 0.236 2759 Planarity : 0.004 0.047 2878 Dihedral : 7.113 64.355 2605 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.04 % Favored : 97.91 % Rotamer: Outliers : 1.02 % Allowed : 12.62 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.19), residues: 2005 helix: 2.82 (0.18), residues: 784 sheet: -0.34 (0.25), residues: 390 loop : -0.05 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 446 TYR 0.014 0.001 TYR A 63 PHE 0.020 0.001 PHE A 284 TRP 0.008 0.001 TRP C 311 HIS 0.003 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (17031) covalent geometry : angle 0.51913 / 0.27 (23237) SS BOND : bond 0.00413 / 0.22 ( 6) SS BOND : angle 1.34999 / 0.80 ( 12) hydrogen bonds : bond 0.04074 / 2.72 ( 885) hydrogen bonds : angle 4.15791 / 2.95 ( 2784) link_ALPHA1-3 : bond 0.00703 / 0.34 ( 3) link_ALPHA1-3 : angle 1.64634 / 0.96 ( 9) link_ALPHA1-6 : bond 0.00371 / 0.18 ( 2) link_ALPHA1-6 : angle 1.91703 / 1.09 ( 6) link_BETA1-4 : bond 0.00452 / 0.30 ( 10) link_BETA1-4 : angle 2.31092 / 1.67 ( 30) link_NAG-ASN : bond 0.00389 / 0.19 ( 6) link_NAG-ASN : angle 2.28154 / 1.44 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12924.40 seconds wall clock time: 218 minutes 44.17 seconds (13124.17 seconds total)