Starting phenix.real_space_refine on Thu Sep 26 20:55:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm5_20388/09_2024/6pm5_20388.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm5_20388/09_2024/6pm5_20388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm5_20388/09_2024/6pm5_20388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm5_20388/09_2024/6pm5_20388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm5_20388/09_2024/6pm5_20388.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm5_20388/09_2024/6pm5_20388.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.065 sd= 3.206 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9120 2.51 5 N 2275 2.21 5 O 2480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13975 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2751 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 39 Chain: "G" 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Restraints were copied for chains: C, B, E, D, F, I, H, J Time building chain proxies: 6.25, per 1000 atoms: 0.45 Number of scatterers: 13975 At special positions: 0 Unit cell: (106.167, 106.167, 134.972, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2480 8.00 N 2275 7.00 C 9120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " 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 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 F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 1.9 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 40.3% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.533A pdb=" N ASP A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.834A pdb=" N GLY A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 40' Processing helix chain 'A' and resid 87 through 90 removed outlier: 3.542A pdb=" N ALA A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.642A pdb=" N ASP A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.774A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 264 through 286 removed outlier: 3.506A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 327 removed outlier: 3.610A pdb=" N ILE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 428 removed outlier: 3.608A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.719A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.534A pdb=" N ASP B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.834A pdb=" N GLY B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 40' Processing helix chain 'B' and resid 87 through 90 removed outlier: 3.542A pdb=" N ALA B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 90' Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.641A pdb=" N ASP B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.774A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 264 through 286 removed outlier: 3.506A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 327 removed outlier: 3.609A pdb=" N ILE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 428 removed outlier: 3.607A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.719A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE B 428 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.533A pdb=" N ASP C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.834A pdb=" N GLY C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 40' Processing helix chain 'C' and resid 87 through 90 removed outlier: 3.542A pdb=" N ALA C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 90' Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.643A pdb=" N ASP C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 244 through 256 removed outlier: 3.773A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 259 No H-bonds generated for 'chain 'C' and resid 257 through 259' Processing helix chain 'C' and resid 264 through 286 removed outlier: 3.505A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 327 removed outlier: 3.611A pdb=" N ILE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 428 removed outlier: 3.608A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.720A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE C 427 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE C 428 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 35 removed outlier: 3.533A pdb=" N ASP D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 3.834A pdb=" N GLY D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 36 through 40' Processing helix chain 'D' and resid 87 through 90 removed outlier: 3.542A pdb=" N ALA D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.642A pdb=" N ASP D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 244 through 256 removed outlier: 3.774A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'D' and resid 264 through 286 removed outlier: 3.506A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D 278 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 327 removed outlier: 3.610A pdb=" N ILE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP D 302 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 428 removed outlier: 3.607A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.718A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE D 427 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE D 428 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.533A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 removed outlier: 3.834A pdb=" N GLY E 39 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 36 through 40' Processing helix chain 'E' and resid 87 through 90 removed outlier: 3.542A pdb=" N ALA E 90 " --> pdb=" O PRO E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 90' Processing helix chain 'E' and resid 102 through 107 removed outlier: 3.642A pdb=" N ASP E 107 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 244 through 256 removed outlier: 3.774A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 259 No H-bonds generated for 'chain 'E' and resid 257 through 259' Processing helix chain 'E' and resid 264 through 286 removed outlier: 3.506A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR E 278 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 327 removed outlier: 3.610A pdb=" N ILE E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP E 302 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 428 removed outlier: 3.609A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.719A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE E 427 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE E 428 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.683A pdb=" N LEU A 99 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 136 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.727A pdb=" N ASN A 123 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 removed outlier: 3.566A pdb=" N ARG A 212 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS A 231 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU A 208 " --> pdb=" O HIS A 231 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 216 through 217 removed outlier: 3.807A pdb=" N LYS A 216 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 223 " --> pdb=" O LYS A 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.683A pdb=" N LEU B 99 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 136 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 123 removed outlier: 3.727A pdb=" N ASN B 123 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.567A pdb=" N ARG B 212 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N HIS B 231 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU B 208 " --> pdb=" O HIS B 231 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 216 through 217 removed outlier: 3.807A pdb=" N LYS B 216 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 223 " --> pdb=" O LYS B 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.681A pdb=" N LEU C 99 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE C 136 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 122 through 123 removed outlier: 3.727A pdb=" N ASN C 123 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 114 through 116 removed outlier: 3.566A pdb=" N ARG C 212 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS C 231 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU C 208 " --> pdb=" O HIS C 231 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 216 through 217 removed outlier: 3.807A pdb=" N LYS C 216 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE C 223 " --> pdb=" O LYS C 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.682A pdb=" N LEU D 99 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D 136 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 122 through 123 removed outlier: 3.727A pdb=" N ASN D 123 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 114 through 116 removed outlier: 3.566A pdb=" N ARG D 212 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N HIS D 231 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU D 208 " --> pdb=" O HIS D 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 216 through 217 removed outlier: 3.807A pdb=" N LYS D 216 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 223 " --> pdb=" O LYS D 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 99 through 100 removed outlier: 3.682A pdb=" N LEU E 99 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE E 136 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.727A pdb=" N ASN E 123 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 114 through 116 removed outlier: 3.566A pdb=" N ARG E 212 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N HIS E 231 " --> pdb=" O GLU E 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU E 208 " --> pdb=" O HIS E 231 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 216 through 217 removed outlier: 3.807A pdb=" N LYS E 216 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE E 223 " --> pdb=" O LYS E 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 645 hydrogen bonds defined for protein. 1935 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: 4.11 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4285 1.34 - 1.46: 3522 1.46 - 1.58: 6343 1.58 - 1.70: 0 1.70 - 1.81: 170 Bond restraints: 14320 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.77e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 ... (remaining 14315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 19024 1.33 - 2.67: 302 2.67 - 4.00: 69 4.00 - 5.33: 45 5.33 - 6.67: 10 Bond angle restraints: 19450 Sorted by residual: angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.74 6.21 3.00e+00 1.11e-01 4.29e+00 angle pdb=" C3 BMA I 3 " pdb=" C2 BMA I 3 " pdb=" O2 BMA I 3 " ideal model delta sigma weight residual 112.95 106.76 6.19 3.00e+00 1.11e-01 4.26e+00 angle pdb=" C3 BMA J 3 " pdb=" C2 BMA J 3 " pdb=" O2 BMA J 3 " ideal model delta sigma weight residual 112.95 106.77 6.18 3.00e+00 1.11e-01 4.25e+00 angle pdb=" C3 BMA G 3 " pdb=" C2 BMA G 3 " pdb=" O2 BMA G 3 " ideal model delta sigma weight residual 112.95 106.78 6.17 3.00e+00 1.11e-01 4.23e+00 angle pdb=" C3 BMA H 3 " pdb=" C2 BMA H 3 " pdb=" O2 BMA H 3 " ideal model delta sigma weight residual 112.95 106.79 6.16 3.00e+00 1.11e-01 4.22e+00 ... (remaining 19445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 8528 21.72 - 43.44: 120 43.44 - 65.16: 0 65.16 - 86.88: 30 86.88 - 108.60: 20 Dihedral angle restraints: 8698 sinusoidal: 3583 harmonic: 5115 Sorted by residual: dihedral pdb=" O4 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C5 BMA J 3 " pdb=" O5 BMA J 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.89 108.60 1 3.00e+01 1.11e-03 1.41e+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 -179.87 108.58 1 3.00e+01 1.11e-03 1.41e+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 -179.86 108.57 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 8695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 2245 0.197 - 0.393: 5 0.393 - 0.590: 0 0.590 - 0.787: 0 0.787 - 0.984: 5 Chirality restraints: 2255 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-02 2.50e+03 2.42e+03 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-02 2.50e+03 2.42e+03 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-02 2.50e+03 2.42e+03 ... (remaining 2252 not shown) Planarity restraints: 2405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 102 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO E 103 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 102 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO D 103 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 410 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO C 411 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 411 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 411 " 0.017 5.00e-02 4.00e+02 ... (remaining 2402 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 114 2.61 - 3.18: 11340 3.18 - 3.75: 20627 3.75 - 4.33: 29568 4.33 - 4.90: 48189 Nonbonded interactions: 109838 Sorted by model distance: nonbonded pdb=" SG CYS E 214 " pdb=" SG CYS E 225 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS D 214 " pdb=" SG CYS D 225 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS C 214 " pdb=" SG CYS C 225 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS B 214 " pdb=" SG CYS B 225 " model vdw 2.032 3.760 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.275 3.040 ... (remaining 109833 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.100 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 : 0.002 0.027 14320 Z= 0.125 Angle : 0.490 6.666 19450 Z= 0.238 Chirality : 0.063 0.984 2255 Planarity : 0.003 0.031 2400 Dihedral : 11.101 108.604 5375 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.15), residues: 1710 helix: -3.74 (0.12), residues: 535 sheet: -2.45 (0.21), residues: 380 loop : -2.45 (0.18), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 422 HIS 0.001 0.000 HIS A 125 PHE 0.003 0.001 PHE A 203 TYR 0.004 0.000 TYR D 74 ARG 0.001 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.6039 (mmp) cc_final: 0.5671 (ppp) REVERT: A 185 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7652 (mt-10) REVERT: A 210 ASP cc_start: 0.7649 (m-30) cc_final: 0.7280 (m-30) REVERT: A 303 MET cc_start: 0.8856 (mmt) cc_final: 0.8599 (mmt) REVERT: A 398 ARG cc_start: 0.7194 (ttm170) cc_final: 0.6366 (mmp80) REVERT: B 105 MET cc_start: 0.6130 (mmp) cc_final: 0.5608 (ppp) REVERT: B 210 ASP cc_start: 0.7667 (m-30) cc_final: 0.7249 (m-30) REVERT: B 303 MET cc_start: 0.8915 (mmt) cc_final: 0.8556 (mmt) REVERT: B 390 GLU cc_start: 0.5402 (mp0) cc_final: 0.4918 (mp0) REVERT: B 398 ARG cc_start: 0.7322 (ttm170) cc_final: 0.6380 (mmp80) REVERT: C 105 MET cc_start: 0.6194 (mmp) cc_final: 0.5614 (ppp) REVERT: C 185 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7485 (mt-10) REVERT: C 210 ASP cc_start: 0.7695 (m-30) cc_final: 0.7494 (m-30) REVERT: C 398 ARG cc_start: 0.7401 (ttm170) cc_final: 0.6614 (mmp80) REVERT: D 105 MET cc_start: 0.5942 (mmp) cc_final: 0.5610 (ppp) REVERT: D 106 LEU cc_start: 0.7783 (tm) cc_final: 0.7406 (tp) REVERT: D 163 MET cc_start: 0.7048 (mpp) cc_final: 0.6787 (mpp) REVERT: D 210 ASP cc_start: 0.7557 (m-30) cc_final: 0.7068 (m-30) REVERT: D 398 ARG cc_start: 0.7451 (ttm170) cc_final: 0.6811 (mmp80) REVERT: E 185 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7667 (mt-10) REVERT: E 210 ASP cc_start: 0.7581 (m-30) cc_final: 0.7154 (m-30) REVERT: E 303 MET cc_start: 0.8951 (mmt) cc_final: 0.8744 (mmt) REVERT: E 398 ARG cc_start: 0.7388 (ttm170) cc_final: 0.6551 (mmp80) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.2962 time to fit residues: 145.2136 Evaluate side-chains 263 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 51 optimal weight: 0.0030 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 154 optimal weight: 0.3980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 193 GLN A 235 GLN B 166 GLN C 141 ASN C 166 GLN C 193 GLN D 82 GLN D 139 ASN D 166 GLN D 235 GLN E 82 GLN E 139 ASN E 166 GLN E 180 ASN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14320 Z= 0.198 Angle : 0.643 7.215 19450 Z= 0.320 Chirality : 0.046 0.148 2255 Planarity : 0.004 0.044 2400 Dihedral : 8.248 57.022 2190 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.64 % Allowed : 9.29 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.18), residues: 1710 helix: -1.47 (0.19), residues: 610 sheet: -1.38 (0.24), residues: 380 loop : -2.33 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 84 HIS 0.003 0.001 HIS A 125 PHE 0.009 0.001 PHE B 124 TYR 0.018 0.001 TYR C 238 ARG 0.006 0.001 ARG C 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 341 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8131 (t0) cc_final: 0.7898 (t0) REVERT: A 180 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8127 (p0) REVERT: A 181 ASP cc_start: 0.8500 (m-30) cc_final: 0.8274 (m-30) REVERT: A 398 ARG cc_start: 0.6983 (ttm170) cc_final: 0.5931 (mmp80) REVERT: B 41 ASP cc_start: 0.8102 (t0) cc_final: 0.7873 (t0) REVERT: B 91 TYR cc_start: 0.8405 (p90) cc_final: 0.8043 (p90) REVERT: B 141 ASN cc_start: 0.8355 (m-40) cc_final: 0.8044 (m-40) REVERT: B 163 MET cc_start: 0.7520 (mpp) cc_final: 0.6654 (mpp) REVERT: B 210 ASP cc_start: 0.7706 (m-30) cc_final: 0.7054 (m-30) REVERT: B 214 CYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7531 (p) REVERT: B 398 ARG cc_start: 0.7073 (ttm170) cc_final: 0.6047 (mmp80) REVERT: C 185 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7542 (mt-10) REVERT: C 214 CYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7443 (p) REVERT: C 398 ARG cc_start: 0.7198 (ttm170) cc_final: 0.6353 (mmp80) REVERT: D 163 MET cc_start: 0.7285 (mpp) cc_final: 0.6448 (mpp) REVERT: D 398 ARG cc_start: 0.7248 (ttm170) cc_final: 0.6515 (mmp80) REVERT: E 105 MET cc_start: 0.7097 (ppp) cc_final: 0.6321 (ppp) REVERT: E 163 MET cc_start: 0.7513 (mpp) cc_final: 0.6624 (mpp) REVERT: E 185 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7748 (mt-10) REVERT: E 210 ASP cc_start: 0.7519 (m-30) cc_final: 0.7076 (m-30) REVERT: E 398 ARG cc_start: 0.7166 (ttm170) cc_final: 0.6283 (mmp80) outliers start: 39 outliers final: 21 residues processed: 362 average time/residue: 0.2874 time to fit residues: 145.2460 Evaluate side-chains 307 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 283 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 137 optimal weight: 0.0270 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 139 ASN A 193 GLN B 82 GLN C 82 GLN D 219 ASN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14320 Z= 0.230 Angle : 0.622 7.425 19450 Z= 0.305 Chirality : 0.045 0.146 2255 Planarity : 0.004 0.041 2400 Dihedral : 5.643 30.808 2190 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.80 % Allowed : 9.97 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.19), residues: 1710 helix: -0.37 (0.21), residues: 610 sheet: -0.75 (0.25), residues: 370 loop : -2.21 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 422 HIS 0.003 0.001 HIS A 231 PHE 0.013 0.001 PHE C 311 TYR 0.017 0.002 TYR A 144 ARG 0.007 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 293 time to evaluate : 1.642 Fit side-chains REVERT: A 163 MET cc_start: 0.7526 (mpp) cc_final: 0.6750 (mpp) REVERT: A 177 TYR cc_start: 0.8768 (m-80) cc_final: 0.8454 (m-80) REVERT: A 180 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8118 (p0) REVERT: A 181 ASP cc_start: 0.8494 (m-30) cc_final: 0.8210 (m-30) REVERT: A 193 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7838 (mt0) REVERT: A 398 ARG cc_start: 0.6968 (ttm170) cc_final: 0.5925 (mmp80) REVERT: B 91 TYR cc_start: 0.8633 (p90) cc_final: 0.8300 (p90) REVERT: B 235 GLN cc_start: 0.8319 (mm-40) cc_final: 0.7870 (mm-40) REVERT: B 398 ARG cc_start: 0.7012 (ttm170) cc_final: 0.5960 (mmp80) REVERT: C 214 CYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8192 (p) REVERT: C 398 ARG cc_start: 0.7028 (ttm170) cc_final: 0.6174 (mmp80) REVERT: D 163 MET cc_start: 0.7634 (mpp) cc_final: 0.6620 (mpp) REVERT: D 398 ARG cc_start: 0.7192 (ttm170) cc_final: 0.6436 (mmp80) REVERT: E 28 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6907 (tm-30) REVERT: E 105 MET cc_start: 0.7136 (ppp) cc_final: 0.6516 (ppp) REVERT: E 177 TYR cc_start: 0.8807 (m-80) cc_final: 0.8445 (m-80) REVERT: E 185 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7532 (mt-10) REVERT: E 398 ARG cc_start: 0.7159 (ttm170) cc_final: 0.6314 (mmp80) outliers start: 56 outliers final: 37 residues processed: 329 average time/residue: 0.2447 time to fit residues: 117.9722 Evaluate side-chains 306 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 266 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 405 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 193 GLN B 139 ASN C 219 ASN D 219 ASN E 219 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14320 Z= 0.207 Angle : 0.587 6.972 19450 Z= 0.290 Chirality : 0.044 0.158 2255 Planarity : 0.003 0.043 2400 Dihedral : 4.919 19.145 2190 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.12 % Allowed : 13.15 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1710 helix: 0.14 (0.22), residues: 610 sheet: -0.22 (0.27), residues: 345 loop : -2.05 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 84 HIS 0.002 0.001 HIS B 231 PHE 0.010 0.001 PHE E 29 TYR 0.016 0.001 TYR D 317 ARG 0.003 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 285 time to evaluate : 1.530 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.7449 (mpp) cc_final: 0.6900 (mpp) REVERT: A 177 TYR cc_start: 0.8794 (m-80) cc_final: 0.8512 (m-80) REVERT: A 180 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8096 (p0) REVERT: A 181 ASP cc_start: 0.8498 (m-30) cc_final: 0.8219 (m-30) REVERT: A 398 ARG cc_start: 0.6955 (ttm170) cc_final: 0.5933 (mmp80) REVERT: B 398 ARG cc_start: 0.7039 (ttm170) cc_final: 0.5997 (mmp80) REVERT: C 314 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6488 (tt) REVERT: C 398 ARG cc_start: 0.7020 (ttm170) cc_final: 0.6226 (mmp80) REVERT: D 398 ARG cc_start: 0.7148 (ttm170) cc_final: 0.6416 (mmp80) REVERT: E 28 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6871 (tm-30) REVERT: E 105 MET cc_start: 0.7236 (ppp) cc_final: 0.6616 (ppp) REVERT: E 177 TYR cc_start: 0.8842 (m-80) cc_final: 0.8595 (m-80) REVERT: E 185 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7579 (mt-10) REVERT: E 398 ARG cc_start: 0.7136 (ttm170) cc_final: 0.6331 (mmp80) outliers start: 46 outliers final: 35 residues processed: 309 average time/residue: 0.2363 time to fit residues: 108.3923 Evaluate side-chains 309 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 272 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN C 219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14320 Z= 0.237 Angle : 0.589 6.358 19450 Z= 0.292 Chirality : 0.044 0.165 2255 Planarity : 0.003 0.043 2400 Dihedral : 4.628 20.736 2190 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.73 % Allowed : 14.92 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.20), residues: 1710 helix: 0.44 (0.22), residues: 610 sheet: -0.05 (0.27), residues: 350 loop : -1.89 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 84 HIS 0.002 0.001 HIS A 231 PHE 0.011 0.001 PHE A 115 TYR 0.018 0.002 TYR B 144 ARG 0.003 0.000 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 278 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7583 (t70) cc_final: 0.7251 (t70) REVERT: A 177 TYR cc_start: 0.8822 (m-80) cc_final: 0.8484 (m-80) REVERT: A 180 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8102 (p0) REVERT: A 181 ASP cc_start: 0.8493 (m-30) cc_final: 0.8193 (m-30) REVERT: A 398 ARG cc_start: 0.6940 (ttm170) cc_final: 0.5980 (mmp80) REVERT: B 91 TYR cc_start: 0.8807 (p90) cc_final: 0.8543 (p90) REVERT: B 104 SER cc_start: 0.8310 (m) cc_final: 0.8037 (p) REVERT: B 105 MET cc_start: 0.6876 (mmp) cc_final: 0.6671 (mmp) REVERT: B 177 TYR cc_start: 0.8866 (m-80) cc_final: 0.8440 (m-80) REVERT: B 219 ASN cc_start: 0.8145 (p0) cc_final: 0.7944 (p0) REVERT: B 398 ARG cc_start: 0.7082 (ttm170) cc_final: 0.6042 (mmp80) REVERT: C 177 TYR cc_start: 0.8882 (m-80) cc_final: 0.8601 (m-80) REVERT: C 185 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7626 (mt-10) REVERT: C 314 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6620 (tt) REVERT: C 398 ARG cc_start: 0.6990 (ttm170) cc_final: 0.6236 (mmp80) REVERT: D 398 ARG cc_start: 0.7134 (ttm170) cc_final: 0.6423 (mmp80) REVERT: D 401 ARG cc_start: 0.6959 (tpt170) cc_final: 0.6589 (ttm-80) REVERT: E 28 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6905 (tm-30) REVERT: E 105 MET cc_start: 0.7240 (ppp) cc_final: 0.6650 (ppp) REVERT: E 177 TYR cc_start: 0.8907 (m-80) cc_final: 0.8651 (m-80) REVERT: E 185 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7555 (mt-10) REVERT: E 398 ARG cc_start: 0.7173 (ttm170) cc_final: 0.6389 (mmp80) outliers start: 55 outliers final: 43 residues processed: 308 average time/residue: 0.2442 time to fit residues: 110.3653 Evaluate side-chains 317 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 272 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 0.0970 chunk 40 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14320 Z= 0.217 Angle : 0.580 7.381 19450 Z= 0.287 Chirality : 0.044 0.169 2255 Planarity : 0.003 0.041 2400 Dihedral : 4.523 20.494 2190 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.86 % Allowed : 15.80 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1710 helix: 0.61 (0.23), residues: 610 sheet: 0.22 (0.28), residues: 350 loop : -1.80 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 84 HIS 0.002 0.001 HIS A 231 PHE 0.010 0.001 PHE A 115 TYR 0.018 0.002 TYR D 317 ARG 0.007 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 276 time to evaluate : 1.603 Fit side-chains revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7636 (t70) cc_final: 0.7307 (t70) REVERT: A 177 TYR cc_start: 0.8820 (m-80) cc_final: 0.8482 (m-80) REVERT: A 180 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8101 (p0) REVERT: A 181 ASP cc_start: 0.8475 (m-30) cc_final: 0.8185 (m-30) REVERT: A 398 ARG cc_start: 0.6926 (ttm170) cc_final: 0.5968 (mmp80) REVERT: B 91 TYR cc_start: 0.8849 (p90) cc_final: 0.8552 (p90) REVERT: B 177 TYR cc_start: 0.8861 (m-80) cc_final: 0.8429 (m-80) REVERT: B 398 ARG cc_start: 0.7061 (ttm170) cc_final: 0.6074 (mmp80) REVERT: C 102 ASP cc_start: 0.7801 (t70) cc_final: 0.7555 (t70) REVERT: C 177 TYR cc_start: 0.8885 (m-80) cc_final: 0.8643 (m-80) REVERT: C 185 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7625 (mt-10) REVERT: C 398 ARG cc_start: 0.6974 (ttm170) cc_final: 0.6271 (mmp80) REVERT: D 398 ARG cc_start: 0.7152 (ttm170) cc_final: 0.6420 (mmp80) REVERT: D 401 ARG cc_start: 0.6946 (tpt170) cc_final: 0.6588 (ttm-80) REVERT: E 28 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6915 (tm-30) REVERT: E 105 MET cc_start: 0.7256 (ppp) cc_final: 0.6606 (ppp) REVERT: E 177 TYR cc_start: 0.8914 (m-80) cc_final: 0.8655 (m-80) REVERT: E 185 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7554 (mt-10) REVERT: E 253 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6810 (mp) REVERT: E 398 ARG cc_start: 0.7129 (ttm170) cc_final: 0.6379 (mmp80) outliers start: 57 outliers final: 44 residues processed: 306 average time/residue: 0.2489 time to fit residues: 112.4709 Evaluate side-chains 314 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 268 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 405 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 chunk 163 optimal weight: 0.1980 chunk 102 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14320 Z= 0.169 Angle : 0.572 7.421 19450 Z= 0.280 Chirality : 0.043 0.172 2255 Planarity : 0.003 0.039 2400 Dihedral : 4.312 20.461 2190 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.53 % Allowed : 16.07 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1710 helix: 0.78 (0.23), residues: 610 sheet: 0.36 (0.28), residues: 350 loop : -1.67 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 84 HIS 0.002 0.000 HIS B 231 PHE 0.013 0.001 PHE C 311 TYR 0.016 0.001 TYR D 317 ARG 0.003 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 290 time to evaluate : 1.472 Fit side-chains revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7697 (t70) cc_final: 0.7370 (t70) REVERT: A 177 TYR cc_start: 0.8797 (m-80) cc_final: 0.8445 (m-80) REVERT: A 180 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8049 (p0) REVERT: A 181 ASP cc_start: 0.8459 (m-30) cc_final: 0.8144 (m-30) REVERT: A 193 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7853 (mt0) REVERT: A 398 ARG cc_start: 0.6915 (ttm170) cc_final: 0.5961 (mmp80) REVERT: B 91 TYR cc_start: 0.8806 (p90) cc_final: 0.8537 (p90) REVERT: B 177 TYR cc_start: 0.8838 (m-80) cc_final: 0.8431 (m-80) REVERT: B 398 ARG cc_start: 0.7020 (ttm170) cc_final: 0.6061 (mmp80) REVERT: C 93 GLU cc_start: 0.7253 (pm20) cc_final: 0.6760 (pm20) REVERT: C 102 ASP cc_start: 0.7862 (t70) cc_final: 0.7600 (t70) REVERT: C 177 TYR cc_start: 0.8857 (m-80) cc_final: 0.8588 (m-80) REVERT: C 185 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7619 (mt-10) REVERT: C 398 ARG cc_start: 0.6991 (ttm170) cc_final: 0.6306 (mmp80) REVERT: D 102 ASP cc_start: 0.7730 (t70) cc_final: 0.7522 (t70) REVERT: D 398 ARG cc_start: 0.7150 (ttm170) cc_final: 0.6423 (mmp80) REVERT: D 401 ARG cc_start: 0.6981 (tpt170) cc_final: 0.6605 (ttm-80) REVERT: E 28 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6960 (tm-30) REVERT: E 105 MET cc_start: 0.7249 (ppp) cc_final: 0.6560 (ppp) REVERT: E 177 TYR cc_start: 0.8896 (m-80) cc_final: 0.8650 (m-80) REVERT: E 185 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7508 (mt-10) REVERT: E 225 CYS cc_start: 0.8859 (t) cc_final: 0.8523 (t) REVERT: E 236 MET cc_start: 0.7785 (mmm) cc_final: 0.6894 (mmm) REVERT: E 398 ARG cc_start: 0.7114 (ttm170) cc_final: 0.6372 (mmp80) outliers start: 52 outliers final: 41 residues processed: 310 average time/residue: 0.2338 time to fit residues: 107.3776 Evaluate side-chains 314 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 271 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 111 optimal weight: 0.0570 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN C 321 ASN D 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14320 Z= 0.310 Angle : 0.645 7.542 19450 Z= 0.322 Chirality : 0.046 0.174 2255 Planarity : 0.004 0.042 2400 Dihedral : 4.663 20.397 2190 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.00 % Allowed : 16.27 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.21), residues: 1710 helix: 0.59 (0.22), residues: 625 sheet: 0.37 (0.29), residues: 350 loop : -1.55 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 302 HIS 0.003 0.001 HIS B 231 PHE 0.013 0.002 PHE B 124 TYR 0.019 0.002 TYR D 317 ARG 0.003 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 262 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7815 (t70) cc_final: 0.7553 (t70) REVERT: A 177 TYR cc_start: 0.8853 (m-80) cc_final: 0.8432 (m-80) REVERT: A 180 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8098 (p0) REVERT: A 181 ASP cc_start: 0.8501 (m-30) cc_final: 0.8213 (m-30) REVERT: A 398 ARG cc_start: 0.6954 (ttm170) cc_final: 0.6022 (mmp80) REVERT: B 316 GLU cc_start: 0.8306 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 398 ARG cc_start: 0.7080 (ttm170) cc_final: 0.6149 (mmp80) REVERT: C 93 GLU cc_start: 0.7356 (pm20) cc_final: 0.7090 (pm20) REVERT: C 102 ASP cc_start: 0.7983 (t70) cc_final: 0.7613 (t70) REVERT: C 105 MET cc_start: 0.7264 (mmp) cc_final: 0.6644 (ppp) REVERT: C 170 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8253 (ptp) REVERT: C 177 TYR cc_start: 0.8913 (m-80) cc_final: 0.8625 (m-80) REVERT: C 185 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7606 (mt-10) REVERT: C 253 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6899 (mp) REVERT: C 398 ARG cc_start: 0.7038 (ttm170) cc_final: 0.6375 (mmp80) REVERT: D 398 ARG cc_start: 0.7170 (ttm170) cc_final: 0.6459 (mmp80) REVERT: D 401 ARG cc_start: 0.6997 (tpt170) cc_final: 0.6624 (ttm-80) REVERT: E 105 MET cc_start: 0.7305 (ppp) cc_final: 0.6490 (ppp) REVERT: E 177 TYR cc_start: 0.8938 (m-80) cc_final: 0.8633 (m-80) REVERT: E 185 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7539 (mt-10) REVERT: E 253 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6717 (mp) REVERT: E 279 MET cc_start: 0.8972 (mmm) cc_final: 0.8602 (tpt) REVERT: E 398 ARG cc_start: 0.7137 (ttm170) cc_final: 0.6390 (mmp80) outliers start: 59 outliers final: 46 residues processed: 294 average time/residue: 0.2481 time to fit residues: 107.5177 Evaluate side-chains 305 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 255 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 294 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 137 optimal weight: 0.0170 chunk 144 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 161 optimal weight: 0.5980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14320 Z= 0.182 Angle : 0.596 8.601 19450 Z= 0.291 Chirality : 0.044 0.176 2255 Planarity : 0.003 0.039 2400 Dihedral : 4.399 20.631 2190 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.12 % Allowed : 17.69 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.21), residues: 1710 helix: 0.77 (0.22), residues: 625 sheet: 0.44 (0.29), residues: 350 loop : -1.49 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 84 HIS 0.002 0.001 HIS A 231 PHE 0.012 0.001 PHE C 311 TYR 0.017 0.001 TYR D 317 ARG 0.002 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 268 time to evaluate : 1.678 Fit side-chains revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7792 (t70) cc_final: 0.7553 (t70) REVERT: A 177 TYR cc_start: 0.8812 (m-80) cc_final: 0.8417 (m-80) REVERT: A 180 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8062 (p0) REVERT: A 181 ASP cc_start: 0.8486 (m-30) cc_final: 0.8194 (m-30) REVERT: A 236 MET cc_start: 0.7282 (mmm) cc_final: 0.6668 (mmm) REVERT: A 398 ARG cc_start: 0.6925 (ttm170) cc_final: 0.6042 (mmp80) REVERT: B 91 TYR cc_start: 0.8796 (p90) cc_final: 0.8595 (p90) REVERT: B 398 ARG cc_start: 0.7068 (ttm170) cc_final: 0.6127 (mmp80) REVERT: C 93 GLU cc_start: 0.7307 (pm20) cc_final: 0.7017 (pm20) REVERT: C 102 ASP cc_start: 0.7976 (t70) cc_final: 0.7746 (t70) REVERT: C 170 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8164 (ptp) REVERT: C 177 TYR cc_start: 0.8866 (m-80) cc_final: 0.8623 (m-80) REVERT: C 185 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7625 (mt-10) REVERT: C 398 ARG cc_start: 0.7016 (ttm170) cc_final: 0.6376 (mmp80) REVERT: D 398 ARG cc_start: 0.7156 (ttm170) cc_final: 0.6468 (mmp80) REVERT: D 401 ARG cc_start: 0.6986 (tpt170) cc_final: 0.6604 (ttm-80) REVERT: E 105 MET cc_start: 0.7326 (ppp) cc_final: 0.6986 (ppp) REVERT: E 177 TYR cc_start: 0.8885 (m-80) cc_final: 0.8620 (m-80) REVERT: E 185 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7545 (mt-10) REVERT: E 225 CYS cc_start: 0.8823 (t) cc_final: 0.8466 (t) REVERT: E 279 MET cc_start: 0.8957 (mmm) cc_final: 0.8678 (tpt) REVERT: E 398 ARG cc_start: 0.7100 (ttm170) cc_final: 0.6369 (mmp80) outliers start: 46 outliers final: 36 residues processed: 289 average time/residue: 0.2617 time to fit residues: 112.0893 Evaluate side-chains 306 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 268 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 294 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.6980 chunk 76 optimal weight: 0.0970 chunk 112 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 104 optimal weight: 0.0770 chunk 82 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14320 Z= 0.176 Angle : 0.596 9.155 19450 Z= 0.290 Chirality : 0.044 0.175 2255 Planarity : 0.003 0.039 2400 Dihedral : 4.317 20.429 2190 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.85 % Allowed : 18.31 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1710 helix: 0.89 (0.22), residues: 615 sheet: 0.62 (0.29), residues: 345 loop : -1.48 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 84 HIS 0.002 0.001 HIS D 231 PHE 0.012 0.001 PHE A 258 TYR 0.016 0.001 TYR D 317 ARG 0.002 0.000 ARG A 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 276 time to evaluate : 1.715 Fit side-chains revert: symmetry clash REVERT: A 102 ASP cc_start: 0.7813 (t70) cc_final: 0.7595 (t70) REVERT: A 177 TYR cc_start: 0.8797 (m-80) cc_final: 0.8398 (m-80) REVERT: A 180 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.8030 (p0) REVERT: A 181 ASP cc_start: 0.8499 (m-30) cc_final: 0.8198 (m-30) REVERT: A 193 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7789 (mt0) REVERT: A 276 VAL cc_start: 0.7819 (p) cc_final: 0.7590 (p) REVERT: A 398 ARG cc_start: 0.6919 (ttm170) cc_final: 0.6041 (mmp80) REVERT: B 177 TYR cc_start: 0.8842 (m-80) cc_final: 0.8393 (m-80) REVERT: B 398 ARG cc_start: 0.7062 (ttm170) cc_final: 0.6127 (mmp80) REVERT: C 170 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8213 (ptp) REVERT: C 177 TYR cc_start: 0.8856 (m-80) cc_final: 0.8622 (m-80) REVERT: C 398 ARG cc_start: 0.7015 (ttm170) cc_final: 0.6379 (mmp80) REVERT: D 398 ARG cc_start: 0.7144 (ttm170) cc_final: 0.6480 (mmp80) REVERT: D 401 ARG cc_start: 0.6986 (tpt170) cc_final: 0.6605 (ttm-80) REVERT: E 105 MET cc_start: 0.7335 (ppp) cc_final: 0.6955 (ppp) REVERT: E 177 TYR cc_start: 0.8890 (m-80) cc_final: 0.8607 (m-80) REVERT: E 398 ARG cc_start: 0.7094 (ttm170) cc_final: 0.6362 (mmp80) outliers start: 42 outliers final: 34 residues processed: 295 average time/residue: 0.2364 time to fit residues: 103.6850 Evaluate side-chains 305 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 268 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.140294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.113210 restraints weight = 17459.271| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.85 r_work: 0.3117 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.309 14320 Z= 0.374 Angle : 0.810 65.899 19450 Z= 0.449 Chirality : 0.047 0.854 2255 Planarity : 0.006 0.260 2400 Dihedral : 4.327 20.424 2190 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.71 % Allowed : 18.51 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1710 helix: 0.88 (0.22), residues: 615 sheet: 0.62 (0.29), residues: 345 loop : -1.47 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 84 HIS 0.001 0.001 HIS D 231 PHE 0.011 0.001 PHE A 258 TYR 0.017 0.001 TYR D 317 ARG 0.001 0.000 ARG D 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3219.82 seconds wall clock time: 58 minutes 26.32 seconds (3506.32 seconds total)