Starting phenix.real_space_refine on Thu Feb 5 16:09:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yy6_39670/02_2026/8yy6_39670.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yy6_39670/02_2026/8yy6_39670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yy6_39670/02_2026/8yy6_39670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yy6_39670/02_2026/8yy6_39670.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yy6_39670/02_2026/8yy6_39670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yy6_39670/02_2026/8yy6_39670.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 87 5.16 5 C 11451 2.51 5 N 3087 2.21 5 O 3558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18183 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 4348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4348 Classifications: {'peptide': 556} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 539} Chain breaks: 5 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 5, 'HIS:plan': 1, 'ASP:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: E, G, H, I, B, C Time building chain proxies: 4.54, per 1000 atoms: 0.25 Number of scatterers: 18183 At special positions: 0 Unit cell: (167.44, 156.4, 175.72, 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 87 16.00 O 3558 8.00 N 3087 7.00 C 11451 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS A 178 " - pdb=" SG CYS A 918 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 467 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 87 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 178 " - pdb=" SG CYS B 918 " distance=2.03 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 918 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 467 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 467 " 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 NAG-ASN " NAG A1301 " - " ASN A 415 " " NAG B1301 " - " ASN B 415 " " NAG C1301 " - " ASN C 415 " Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 822.9 milliseconds 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 39 sheets defined 18.0% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'F' and resid 78 through 82 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.763A pdb=" N GLN A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.707A pdb=" N ARG A 390 " --> pdb=" O TYR A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 467 through 484 removed outlier: 4.499A pdb=" N GLN A 471 " --> pdb=" O CYS A 467 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 974 removed outlier: 3.537A pdb=" N GLN A 887 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET A 945 " --> pdb=" O LYS A 922 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 974 " --> pdb=" O ARG A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 996 Processing helix chain 'A' and resid 1170 through 1174 Processing helix chain 'A' and resid 1200 through 1206 Processing helix chain 'A' and resid 1211 through 1231 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'H' and resid 78 through 82 Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.763A pdb=" N GLN B 259 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR B 262 " --> pdb=" O ASP B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.706A pdb=" N ARG B 390 " --> pdb=" O TYR B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 467 through 484 removed outlier: 4.499A pdb=" N GLN B 471 " --> pdb=" O CYS B 467 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 974 removed outlier: 3.537A pdb=" N GLN B 887 " --> pdb=" O SER B 883 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET B 945 " --> pdb=" O LYS B 922 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS B 974 " --> pdb=" O ARG B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 996 Processing helix chain 'B' and resid 1170 through 1174 Processing helix chain 'B' and resid 1200 through 1206 Processing helix chain 'B' and resid 1211 through 1231 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'I' and resid 78 through 82 Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.762A pdb=" N GLN C 259 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR C 262 " --> pdb=" O ASP C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.707A pdb=" N ARG C 390 " --> pdb=" O TYR C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 467 through 484 removed outlier: 4.499A pdb=" N GLN C 471 " --> pdb=" O CYS C 467 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 482 " --> pdb=" O GLU C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 974 removed outlier: 3.537A pdb=" N GLN C 887 " --> pdb=" O SER C 883 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET C 945 " --> pdb=" O LYS C 922 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS C 974 " --> pdb=" O ARG C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 996 Processing helix chain 'C' and resid 1170 through 1174 Processing helix chain 'C' and resid 1200 through 1206 Processing helix chain 'C' and resid 1211 through 1231 Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.108A pdb=" N GLU D 10 " --> pdb=" O THR D 113 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE D 34 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN D 59 " --> pdb=" O ASN D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'F' and resid 44 through 47 removed outlier: 6.732A pdb=" N TRP F 34 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1000 through 1002 removed outlier: 3.725A pdb=" N ALA A1000 " --> pdb=" O SER A1021 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A1019 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU C1177 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG A 171 " --> pdb=" O LEU C1177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 449 through 453 removed outlier: 3.886A pdb=" N ILE A 440 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP A 425 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LYS A 196 " --> pdb=" O TRP A 425 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N THR A 427 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL A 194 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASP A 429 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU A 192 " --> pdb=" O ASP A 429 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR A 431 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 190 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 13.713A pdb=" N HIS A 187 " --> pdb=" O PRO A 797 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU A 189 " --> pdb=" O LEU A 795 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 449 through 453 removed outlier: 3.886A pdb=" N ILE A 440 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP A 425 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LYS A 196 " --> pdb=" O TRP A 425 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N THR A 427 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL A 194 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASP A 429 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU A 192 " --> pdb=" O ASP A 429 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR A 431 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 190 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 13.713A pdb=" N HIS A 187 " --> pdb=" O PRO A 797 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU A 189 " --> pdb=" O LEU A 795 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 244 through 250 removed outlier: 7.258A pdb=" N ASN A 244 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU A 232 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 294 through 296 removed outlier: 4.434A pdb=" N ARG A 305 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 304 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LYS A 220 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS A 412 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLU A 397 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 265 through 267 Processing sheet with id=AB2, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AB3, first strand: chain 'A' and resid 1061 through 1064 Processing sheet with id=AB4, first strand: chain 'A' and resid 1151 through 1153 removed outlier: 6.712A pdb=" N ILE A1157 " --> pdb=" O THR A1168 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR A1168 " --> pdb=" O ILE A1157 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL A1159 " --> pdb=" O PHE A1166 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A1166 " --> pdb=" O VAL A1159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1176 through 1177 removed outlier: 3.694A pdb=" N SER B1019 " --> pdb=" O LYS B1002 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B1000 " --> pdb=" O SER B1021 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.108A pdb=" N GLU E 10 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE E 34 " --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN E 59 " --> pdb=" O ASN E 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'H' and resid 44 through 47 removed outlier: 6.731A pdb=" N TRP H 34 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 449 through 453 removed outlier: 3.886A pdb=" N ILE B 440 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TRP B 425 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LYS B 196 " --> pdb=" O TRP B 425 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N THR B 427 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL B 194 " --> pdb=" O THR B 427 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASP B 429 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU B 192 " --> pdb=" O ASP B 429 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B 431 " --> pdb=" O GLY B 190 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 190 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 13.712A pdb=" N HIS B 187 " --> pdb=" O PRO B 797 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU B 189 " --> pdb=" O LEU B 795 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 449 through 453 removed outlier: 3.886A pdb=" N ILE B 440 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TRP B 425 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LYS B 196 " --> pdb=" O TRP B 425 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N THR B 427 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL B 194 " --> pdb=" O THR B 427 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASP B 429 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU B 192 " --> pdb=" O ASP B 429 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B 431 " --> pdb=" O GLY B 190 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 190 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 13.712A pdb=" N HIS B 187 " --> pdb=" O PRO B 797 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU B 189 " --> pdb=" O LEU B 795 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 244 through 250 removed outlier: 7.258A pdb=" N ASN B 244 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU B 232 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 294 through 296 removed outlier: 4.434A pdb=" N ARG B 305 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG B 304 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LYS B 220 " --> pdb=" O LYS B 412 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS B 412 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLU B 397 " --> pdb=" O ASN B 381 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 265 through 267 Processing sheet with id=AC6, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AC7, first strand: chain 'B' and resid 1061 through 1064 Processing sheet with id=AC8, first strand: chain 'B' and resid 1151 through 1153 removed outlier: 6.712A pdb=" N ILE B1157 " --> pdb=" O THR B1168 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR B1168 " --> pdb=" O ILE B1157 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL B1159 " --> pdb=" O PHE B1166 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B1166 " --> pdb=" O VAL B1159 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1176 through 1177 removed outlier: 3.695A pdb=" N SER C1019 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C1000 " --> pdb=" O SER C1021 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.108A pdb=" N GLU G 10 " --> pdb=" O THR G 113 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE G 34 " --> pdb=" O ASN G 50 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN G 59 " --> pdb=" O ASN G 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD4, first strand: chain 'I' and resid 44 through 47 removed outlier: 6.731A pdb=" N TRP I 34 " --> pdb=" O LEU I 46 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 449 through 453 removed outlier: 3.886A pdb=" N ILE C 440 " --> pdb=" O THR C 453 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP C 425 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LYS C 196 " --> pdb=" O TRP C 425 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N THR C 427 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL C 194 " --> pdb=" O THR C 427 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASP C 429 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU C 192 " --> pdb=" O ASP C 429 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR C 431 " --> pdb=" O GLY C 190 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C 190 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 13.713A pdb=" N HIS C 187 " --> pdb=" O PRO C 797 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU C 189 " --> pdb=" O LEU C 795 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 449 through 453 removed outlier: 3.886A pdb=" N ILE C 440 " --> pdb=" O THR C 453 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP C 425 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LYS C 196 " --> pdb=" O TRP C 425 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N THR C 427 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL C 194 " --> pdb=" O THR C 427 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASP C 429 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU C 192 " --> pdb=" O ASP C 429 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR C 431 " --> pdb=" O GLY C 190 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C 190 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 13.713A pdb=" N HIS C 187 " --> pdb=" O PRO C 797 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU C 189 " --> pdb=" O LEU C 795 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 244 through 250 removed outlier: 7.259A pdb=" N ASN C 244 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU C 232 " --> pdb=" O ASN C 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 294 through 296 removed outlier: 4.434A pdb=" N ARG C 305 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG C 304 " --> pdb=" O ASP C 335 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LYS C 220 " --> pdb=" O LYS C 412 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS C 412 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLU C 397 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 265 through 267 Processing sheet with id=AE1, first strand: chain 'C' and resid 269 through 271 Processing sheet with id=AE2, first strand: chain 'C' and resid 1061 through 1064 Processing sheet with id=AE3, first strand: chain 'C' and resid 1151 through 1153 removed outlier: 6.712A pdb=" N ILE C1157 " --> pdb=" O THR C1168 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR C1168 " --> pdb=" O ILE C1157 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL C1159 " --> pdb=" O PHE C1166 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C1166 " --> pdb=" O VAL C1159 " (cutoff:3.500A) 767 hydrogen bonds defined for protein. 2004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5242 1.33 - 1.45: 3296 1.45 - 1.57: 9888 1.57 - 1.69: 0 1.69 - 1.82: 138 Bond restraints: 18564 Sorted by residual: bond pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.66e+00 bond pdb=" N ILE D 51 " pdb=" CA ILE D 51 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.62e+00 bond pdb=" N ILE G 51 " pdb=" CA ILE G 51 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.56e+00 bond pdb=" N VAL G 72 " pdb=" CA VAL G 72 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.17e-02 7.31e+03 8.24e+00 bond pdb=" N TYR G 60 " pdb=" CA TYR G 60 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.16e-02 7.43e+03 8.14e+00 ... (remaining 18559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 24555 1.66 - 3.32: 506 3.32 - 4.97: 88 4.97 - 6.63: 18 6.63 - 8.29: 12 Bond angle restraints: 25179 Sorted by residual: angle pdb=" C GLU B 320 " pdb=" CA GLU B 320 " pdb=" CB GLU B 320 " ideal model delta sigma weight residual 116.34 111.01 5.33 1.40e+00 5.10e-01 1.45e+01 angle pdb=" C GLU A 320 " pdb=" CA GLU A 320 " pdb=" CB GLU A 320 " ideal model delta sigma weight residual 116.34 111.02 5.32 1.40e+00 5.10e-01 1.44e+01 angle pdb=" C GLU C 320 " pdb=" CA GLU C 320 " pdb=" CB GLU C 320 " ideal model delta sigma weight residual 116.34 111.07 5.27 1.40e+00 5.10e-01 1.42e+01 angle pdb=" CA GLY E 49 " pdb=" C GLY E 49 " pdb=" O GLY E 49 " ideal model delta sigma weight residual 121.41 117.95 3.46 9.50e-01 1.11e+00 1.32e+01 angle pdb=" CA ASN G 61 " pdb=" C ASN G 61 " pdb=" O ASN G 61 " ideal model delta sigma weight residual 122.01 118.20 3.81 1.05e+00 9.07e-01 1.32e+01 ... (remaining 25174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 9583 17.59 - 35.18: 1143 35.18 - 52.77: 284 52.77 - 70.36: 54 70.36 - 87.95: 24 Dihedral angle restraints: 11088 sinusoidal: 4287 harmonic: 6801 Sorted by residual: dihedral pdb=" CB CYS A 178 " pdb=" SG CYS A 178 " pdb=" SG CYS A 918 " pdb=" CB CYS A 918 " ideal model delta sinusoidal sigma weight residual 93.00 166.71 -73.71 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS B 178 " pdb=" SG CYS B 178 " pdb=" SG CYS B 918 " pdb=" CB CYS B 918 " ideal model delta sinusoidal sigma weight residual 93.00 166.69 -73.69 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CB CYS C 178 " pdb=" SG CYS C 178 " pdb=" SG CYS C 918 " pdb=" CB CYS C 918 " ideal model delta sinusoidal sigma weight residual 93.00 166.68 -73.68 1 1.00e+01 1.00e-02 6.90e+01 ... (remaining 11085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2080 0.038 - 0.076: 490 0.076 - 0.115: 187 0.115 - 0.153: 57 0.153 - 0.191: 12 Chirality restraints: 2826 Sorted by residual: chirality pdb=" CA ILE G 51 " pdb=" N ILE G 51 " pdb=" C ILE G 51 " pdb=" CB ILE G 51 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA ILE D 51 " pdb=" N ILE D 51 " pdb=" C ILE D 51 " pdb=" CB ILE D 51 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CA ILE E 51 " pdb=" N ILE E 51 " pdb=" C ILE E 51 " pdb=" CB ILE E 51 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 2823 not shown) Planarity restraints: 3231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 13 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO G 14 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO G 14 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 14 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 13 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO D 14 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 13 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO E 14 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " 0.019 5.00e-02 4.00e+02 ... (remaining 3228 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1887 2.75 - 3.29: 16993 3.29 - 3.82: 27430 3.82 - 4.36: 31639 4.36 - 4.90: 56317 Nonbonded interactions: 134266 Sorted by model distance: nonbonded pdb=" OG1 THR B 229 " pdb=" OG1 THR B 328 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THR A 229 " pdb=" OG1 THR A 328 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THR C 229 " pdb=" OG1 THR C 328 " model vdw 2.210 3.040 nonbonded pdb=" OG SER B 430 " pdb=" OE2 GLU B 446 " model vdw 2.249 3.040 nonbonded pdb=" OG SER A 430 " pdb=" OE2 GLU A 446 " model vdw 2.249 3.040 ... (remaining 134261 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: 0.05 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 5.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.210 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18582 Z= 0.216 Angle : 0.588 8.291 25218 Z= 0.340 Chirality : 0.042 0.191 2826 Planarity : 0.003 0.033 3228 Dihedral : 16.442 87.952 6675 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 27.80 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.17), residues: 2286 helix: 1.15 (0.31), residues: 243 sheet: 0.75 (0.21), residues: 633 loop : -1.41 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 60 TYR 0.018 0.001 TYR B1150 PHE 0.013 0.001 PHE B1151 TRP 0.011 0.001 TRP I 90 HIS 0.002 0.001 HIS C 377 Details of bonding type rmsd covalent geometry : bond 0.00354 (18564) covalent geometry : angle 0.58659 (25179) SS BOND : bond 0.00124 ( 15) SS BOND : angle 1.41141 ( 30) hydrogen bonds : bond 0.27607 ( 671) hydrogen bonds : angle 7.62873 ( 2004) link_NAG-ASN : bond 0.00147 ( 3) link_NAG-ASN : angle 0.99561 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.705 Fit side-chains REVERT: D 58 THR cc_start: 0.6538 (p) cc_final: 0.6307 (p) REVERT: D 70 LEU cc_start: 0.9190 (mt) cc_final: 0.8967 (mp) REVERT: D 104 ASP cc_start: 0.8924 (t0) cc_final: 0.8667 (t0) REVERT: A 337 MET cc_start: 0.8969 (mmm) cc_final: 0.8518 (mtt) REVERT: A 1164 HIS cc_start: 0.9190 (m-70) cc_final: 0.8891 (m-70) REVERT: E 58 THR cc_start: 0.6497 (p) cc_final: 0.6231 (p) REVERT: E 104 ASP cc_start: 0.8958 (t0) cc_final: 0.8674 (t0) REVERT: B 337 MET cc_start: 0.8923 (mmm) cc_final: 0.8471 (mtt) REVERT: B 1164 HIS cc_start: 0.9136 (m-70) cc_final: 0.8825 (m-70) REVERT: G 58 THR cc_start: 0.6586 (p) cc_final: 0.6313 (p) REVERT: G 70 LEU cc_start: 0.9165 (mt) cc_final: 0.8942 (mp) REVERT: C 337 MET cc_start: 0.9035 (mmm) cc_final: 0.8690 (mtt) REVERT: C 1164 HIS cc_start: 0.9184 (m-70) cc_final: 0.8885 (m-70) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1708 time to fit residues: 47.6736 Evaluate side-chains 159 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0060 chunk 200 optimal weight: 0.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 976 ASN I 1 GLN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 ASN C1148 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.093633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.056216 restraints weight = 56919.754| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.92 r_work: 0.2902 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18582 Z= 0.117 Angle : 0.541 8.159 25218 Z= 0.282 Chirality : 0.040 0.150 2826 Planarity : 0.003 0.038 3228 Dihedral : 3.900 28.774 2607 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.20 % Allowed : 23.86 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.18), residues: 2286 helix: 2.63 (0.32), residues: 255 sheet: 0.66 (0.20), residues: 732 loop : -1.18 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 76 TYR 0.013 0.001 TYR B1150 PHE 0.013 0.001 PHE B 347 TRP 0.011 0.001 TRP F 90 HIS 0.004 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00252 (18564) covalent geometry : angle 0.54032 (25179) SS BOND : bond 0.00259 ( 15) SS BOND : angle 0.89914 ( 30) hydrogen bonds : bond 0.05470 ( 671) hydrogen bonds : angle 4.68121 ( 2004) link_NAG-ASN : bond 0.00131 ( 3) link_NAG-ASN : angle 0.97263 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 191 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 58 THR cc_start: 0.8268 (p) cc_final: 0.8041 (p) REVERT: D 67 LYS cc_start: 0.9122 (mmmm) cc_final: 0.8820 (mmmm) REVERT: D 83 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8646 (mt) REVERT: D 104 ASP cc_start: 0.9180 (t0) cc_final: 0.8941 (t0) REVERT: A 337 MET cc_start: 0.8570 (mmm) cc_final: 0.8212 (mtt) REVERT: A 779 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.8942 (mm) REVERT: A 1164 HIS cc_start: 0.9334 (m-70) cc_final: 0.9009 (m-70) REVERT: E 58 THR cc_start: 0.8220 (p) cc_final: 0.8010 (p) REVERT: E 97 THR cc_start: 0.9013 (p) cc_final: 0.8625 (p) REVERT: E 104 ASP cc_start: 0.9227 (t0) cc_final: 0.8906 (t0) REVERT: B 779 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9013 (mm) REVERT: B 1164 HIS cc_start: 0.9328 (m-70) cc_final: 0.8998 (m-70) REVERT: G 13 ARG cc_start: 0.8736 (mmm160) cc_final: 0.8413 (mmm160) REVERT: G 58 THR cc_start: 0.8388 (p) cc_final: 0.8181 (p) REVERT: G 81 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7725 (tpt) REVERT: C 337 MET cc_start: 0.8617 (mmm) cc_final: 0.8384 (mtt) REVERT: C 779 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.8924 (mm) REVERT: C 981 MET cc_start: 0.9674 (mmm) cc_final: 0.9471 (mmm) REVERT: C 1164 HIS cc_start: 0.9300 (m-70) cc_final: 0.8978 (m-70) outliers start: 82 outliers final: 42 residues processed: 250 average time/residue: 0.1433 time to fit residues: 54.6434 Evaluate side-chains 216 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 33 TRP Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 976 ASN Chi-restraints excluded: chain A residue 995 TYR Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 995 TYR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 779 ILE Chi-restraints excluded: chain C residue 995 TYR Chi-restraints excluded: chain C residue 1017 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 121 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.0010 chunk 2 optimal weight: 6.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN B 246 HIS C 244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.092945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.056876 restraints weight = 57599.729| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.73 r_work: 0.2818 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 18582 Z= 0.214 Angle : 0.586 6.375 25218 Z= 0.308 Chirality : 0.042 0.168 2826 Planarity : 0.003 0.028 3228 Dihedral : 4.143 29.787 2607 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.71 % Allowed : 24.94 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.18), residues: 2286 helix: 2.86 (0.33), residues: 255 sheet: 0.70 (0.20), residues: 780 loop : -1.36 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1230 TYR 0.015 0.001 TYR A 224 PHE 0.021 0.001 PHE A 347 TRP 0.023 0.002 TRP F 90 HIS 0.004 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00509 (18564) covalent geometry : angle 0.58351 (25179) SS BOND : bond 0.00375 ( 15) SS BOND : angle 1.48084 ( 30) hydrogen bonds : bond 0.06254 ( 671) hydrogen bonds : angle 4.58761 ( 2004) link_NAG-ASN : bond 0.00167 ( 3) link_NAG-ASN : angle 1.26204 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 168 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 23 LYS cc_start: 0.8695 (tppt) cc_final: 0.8265 (tppt) REVERT: D 67 LYS cc_start: 0.9193 (mmmm) cc_final: 0.8827 (mmmm) REVERT: D 104 ASP cc_start: 0.9289 (t0) cc_final: 0.9076 (t0) REVERT: F 38 LYS cc_start: 0.8152 (mmtp) cc_final: 0.7946 (mmtp) REVERT: A 779 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9016 (mt) REVERT: A 1164 HIS cc_start: 0.9329 (m-70) cc_final: 0.8967 (m-70) REVERT: E 23 LYS cc_start: 0.8727 (tppt) cc_final: 0.8338 (tppt) REVERT: E 104 ASP cc_start: 0.9246 (t0) cc_final: 0.8994 (t0) REVERT: B 779 ILE cc_start: 0.9433 (OUTLIER) cc_final: 0.9089 (mt) REVERT: B 1164 HIS cc_start: 0.9331 (m-70) cc_final: 0.8977 (m-70) REVERT: G 23 LYS cc_start: 0.8729 (tppt) cc_final: 0.8400 (tppt) REVERT: G 67 LYS cc_start: 0.9232 (mmmm) cc_final: 0.8861 (mmmm) REVERT: G 81 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7636 (tpt) REVERT: C 337 MET cc_start: 0.8868 (mmm) cc_final: 0.8299 (mtt) REVERT: C 779 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9056 (mm) REVERT: C 1164 HIS cc_start: 0.9315 (m-70) cc_final: 0.8974 (m-70) outliers start: 92 outliers final: 60 residues processed: 243 average time/residue: 0.1372 time to fit residues: 51.6264 Evaluate side-chains 230 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 166 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 33 TRP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 995 TYR Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1186 SER Chi-restraints excluded: chain B residue 1226 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 779 ILE Chi-restraints excluded: chain C residue 1134 PHE Chi-restraints excluded: chain C residue 1150 TYR Chi-restraints excluded: chain C residue 1186 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 117 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 111 optimal weight: 50.0000 chunk 173 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 163 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 976 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.094574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058828 restraints weight = 57590.181| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.73 r_work: 0.2846 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18582 Z= 0.157 Angle : 0.541 6.563 25218 Z= 0.281 Chirality : 0.041 0.150 2826 Planarity : 0.003 0.029 3228 Dihedral : 3.902 28.201 2607 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.56 % Allowed : 25.86 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.18), residues: 2286 helix: 2.99 (0.33), residues: 255 sheet: 0.72 (0.20), residues: 792 loop : -1.35 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 13 TYR 0.018 0.001 TYR I 86 PHE 0.016 0.001 PHE A 347 TRP 0.020 0.001 TRP F 90 HIS 0.003 0.001 HIS C 377 Details of bonding type rmsd covalent geometry : bond 0.00370 (18564) covalent geometry : angle 0.53938 (25179) SS BOND : bond 0.00314 ( 15) SS BOND : angle 1.16821 ( 30) hydrogen bonds : bond 0.05306 ( 671) hydrogen bonds : angle 4.34221 ( 2004) link_NAG-ASN : bond 0.00045 ( 3) link_NAG-ASN : angle 1.11885 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 170 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8813 (mmmm) REVERT: D 104 ASP cc_start: 0.9264 (t0) cc_final: 0.9044 (t0) REVERT: A 271 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8328 (mttt) REVERT: A 779 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.8989 (mt) REVERT: A 1164 HIS cc_start: 0.9323 (m-70) cc_final: 0.8964 (m-70) REVERT: E 13 ARG cc_start: 0.8895 (mmm160) cc_final: 0.8578 (mmp-170) REVERT: E 67 LYS cc_start: 0.9186 (mmmm) cc_final: 0.8802 (mmmm) REVERT: E 104 ASP cc_start: 0.9251 (t0) cc_final: 0.8980 (t0) REVERT: H 32 MET cc_start: 0.8852 (tpp) cc_final: 0.8576 (tpp) REVERT: H 81 ASP cc_start: 0.8038 (m-30) cc_final: 0.7776 (m-30) REVERT: B 271 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8113 (mptt) REVERT: B 779 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9080 (mt) REVERT: B 1164 HIS cc_start: 0.9350 (m-70) cc_final: 0.9007 (m-70) REVERT: G 67 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8850 (mmmm) REVERT: G 81 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7650 (tpt) REVERT: C 271 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8270 (mptt) REVERT: C 337 MET cc_start: 0.8788 (mmm) cc_final: 0.8289 (mtt) REVERT: C 779 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9006 (mm) REVERT: C 1164 HIS cc_start: 0.9312 (m-70) cc_final: 0.8938 (m-70) outliers start: 89 outliers final: 75 residues processed: 244 average time/residue: 0.1406 time to fit residues: 52.9312 Evaluate side-chains 248 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 166 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 33 TRP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 995 TYR Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 995 TYR Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1186 SER Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 467 CYS Chi-restraints excluded: chain C residue 779 ILE Chi-restraints excluded: chain C residue 995 TYR Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain C residue 1134 PHE Chi-restraints excluded: chain C residue 1150 TYR Chi-restraints excluded: chain C residue 1186 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 15 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 chunk 203 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.092869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.056889 restraints weight = 57460.317| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.70 r_work: 0.2811 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18582 Z= 0.217 Angle : 0.588 7.081 25218 Z= 0.305 Chirality : 0.042 0.166 2826 Planarity : 0.003 0.029 3228 Dihedral : 4.116 29.891 2607 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.53 % Allowed : 25.91 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.18), residues: 2286 helix: 2.91 (0.33), residues: 255 sheet: 0.75 (0.20), residues: 780 loop : -1.42 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1003 TYR 0.014 0.001 TYR B 224 PHE 0.019 0.001 PHE A 347 TRP 0.025 0.002 TRP F 90 HIS 0.004 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00517 (18564) covalent geometry : angle 0.58624 (25179) SS BOND : bond 0.00346 ( 15) SS BOND : angle 1.38259 ( 30) hydrogen bonds : bond 0.05787 ( 671) hydrogen bonds : angle 4.40930 ( 2004) link_NAG-ASN : bond 0.00164 ( 3) link_NAG-ASN : angle 1.28223 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 168 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: D 23 LYS cc_start: 0.8615 (tppt) cc_final: 0.8381 (tppt) REVERT: D 67 LYS cc_start: 0.9179 (mmmm) cc_final: 0.8872 (mmmm) REVERT: A 271 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8306 (mttt) REVERT: A 779 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9011 (mm) REVERT: A 1164 HIS cc_start: 0.9321 (m-70) cc_final: 0.8944 (m-70) REVERT: E 4 LEU cc_start: 0.8857 (tp) cc_final: 0.8607 (tp) REVERT: E 5 GLN cc_start: 0.7452 (pm20) cc_final: 0.7239 (pm20) REVERT: E 13 ARG cc_start: 0.8921 (mmm160) cc_final: 0.8517 (mmp-170) REVERT: E 67 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8799 (mmmm) REVERT: E 104 ASP cc_start: 0.9315 (t0) cc_final: 0.9056 (t0) REVERT: H 81 ASP cc_start: 0.8222 (m-30) cc_final: 0.7952 (m-30) REVERT: B 271 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8124 (mptt) REVERT: B 779 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9044 (mm) REVERT: B 1164 HIS cc_start: 0.9343 (m-70) cc_final: 0.8971 (m-70) REVERT: G 67 LYS cc_start: 0.9235 (mmmm) cc_final: 0.8866 (mmmm) REVERT: G 81 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7760 (tpt) REVERT: C 271 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8229 (mptt) REVERT: C 337 MET cc_start: 0.8853 (mmm) cc_final: 0.8330 (mtt) REVERT: C 779 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9081 (mm) REVERT: C 1164 HIS cc_start: 0.9321 (m-70) cc_final: 0.8978 (m-70) outliers start: 108 outliers final: 80 residues processed: 264 average time/residue: 0.1353 time to fit residues: 55.9287 Evaluate side-chains 252 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 165 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 33 TRP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 995 TYR Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 995 TYR Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1186 SER Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 779 ILE Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain C residue 1134 PHE Chi-restraints excluded: chain C residue 1150 TYR Chi-restraints excluded: chain C residue 1186 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 82 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 187 optimal weight: 40.0000 chunk 155 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.093822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.058165 restraints weight = 56971.405| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.72 r_work: 0.2851 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18582 Z= 0.140 Angle : 0.545 8.400 25218 Z= 0.279 Chirality : 0.040 0.154 2826 Planarity : 0.003 0.033 3228 Dihedral : 3.848 27.314 2607 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.86 % Allowed : 26.42 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.18), residues: 2286 helix: 3.06 (0.33), residues: 255 sheet: 0.89 (0.20), residues: 741 loop : -1.35 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C1003 TYR 0.011 0.001 TYR I 86 PHE 0.015 0.001 PHE A 347 TRP 0.019 0.001 TRP F 90 HIS 0.003 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00327 (18564) covalent geometry : angle 0.54399 (25179) SS BOND : bond 0.00324 ( 15) SS BOND : angle 1.12435 ( 30) hydrogen bonds : bond 0.05028 ( 671) hydrogen bonds : angle 4.20676 ( 2004) link_NAG-ASN : bond 0.00016 ( 3) link_NAG-ASN : angle 1.09956 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 169 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8836 (mmmm) REVERT: A 271 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8331 (mttt) REVERT: A 779 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.8971 (mt) REVERT: A 1164 HIS cc_start: 0.9327 (m-70) cc_final: 0.8945 (m-70) REVERT: E 5 GLN cc_start: 0.7366 (pm20) cc_final: 0.7165 (pm20) REVERT: E 13 ARG cc_start: 0.8891 (mmm160) cc_final: 0.8501 (mmp-170) REVERT: E 67 LYS cc_start: 0.9177 (mmmm) cc_final: 0.8791 (mmmm) REVERT: E 104 ASP cc_start: 0.9283 (t0) cc_final: 0.8993 (t0) REVERT: B 271 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8106 (mptt) REVERT: B 779 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9056 (mt) REVERT: B 1164 HIS cc_start: 0.9351 (m-70) cc_final: 0.9005 (m-70) REVERT: G 67 LYS cc_start: 0.9233 (mmmm) cc_final: 0.8879 (mmmm) REVERT: G 81 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7666 (tpt) REVERT: C 271 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8277 (mptt) REVERT: C 337 MET cc_start: 0.8773 (mmm) cc_final: 0.8306 (mtt) REVERT: C 779 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9001 (mm) REVERT: C 1164 HIS cc_start: 0.9310 (m-70) cc_final: 0.8937 (m-70) outliers start: 95 outliers final: 75 residues processed: 249 average time/residue: 0.1358 time to fit residues: 52.8093 Evaluate side-chains 248 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 166 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 33 TRP Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 995 TYR Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 995 TYR Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 467 CYS Chi-restraints excluded: chain C residue 779 ILE Chi-restraints excluded: chain C residue 995 TYR Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain C residue 1134 PHE Chi-restraints excluded: chain C residue 1186 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 227 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 10 optimal weight: 0.0970 chunk 64 optimal weight: 0.3980 chunk 95 optimal weight: 8.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.093526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.057840 restraints weight = 57568.471| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.70 r_work: 0.2816 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18582 Z= 0.204 Angle : 0.590 7.991 25218 Z= 0.305 Chirality : 0.042 0.164 2826 Planarity : 0.003 0.033 3228 Dihedral : 4.067 29.121 2607 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.12 % Allowed : 26.47 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.18), residues: 2286 helix: 2.96 (0.33), residues: 255 sheet: 0.80 (0.20), residues: 774 loop : -1.38 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 13 TYR 0.013 0.001 TYR B 224 PHE 0.019 0.001 PHE A 347 TRP 0.024 0.002 TRP F 90 HIS 0.005 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00486 (18564) covalent geometry : angle 0.58772 (25179) SS BOND : bond 0.00343 ( 15) SS BOND : angle 1.42529 ( 30) hydrogen bonds : bond 0.05586 ( 671) hydrogen bonds : angle 4.29951 ( 2004) link_NAG-ASN : bond 0.00150 ( 3) link_NAG-ASN : angle 1.27757 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 169 time to evaluate : 0.700 Fit side-chains REVERT: D 67 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8833 (mmmm) REVERT: A 271 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8304 (mttt) REVERT: A 779 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9006 (mm) REVERT: A 1164 HIS cc_start: 0.9322 (m-70) cc_final: 0.8944 (m-70) REVERT: E 13 ARG cc_start: 0.8891 (mmm160) cc_final: 0.8471 (mmp-170) REVERT: E 67 LYS cc_start: 0.9222 (mmmm) cc_final: 0.8859 (mmmm) REVERT: E 104 ASP cc_start: 0.9305 (t0) cc_final: 0.9054 (t0) REVERT: E 116 VAL cc_start: 0.5817 (OUTLIER) cc_final: 0.5552 (p) REVERT: B 271 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8141 (mttt) REVERT: B 779 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9046 (mm) REVERT: B 1164 HIS cc_start: 0.9345 (m-70) cc_final: 0.8966 (m-70) REVERT: G 67 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8885 (mmmm) REVERT: C 156 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8308 (t80) REVERT: C 271 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8292 (mptt) REVERT: C 337 MET cc_start: 0.8846 (mmm) cc_final: 0.8311 (mtt) REVERT: C 779 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9078 (mm) REVERT: C 1164 HIS cc_start: 0.9315 (m-70) cc_final: 0.8959 (m-70) outliers start: 100 outliers final: 77 residues processed: 258 average time/residue: 0.1351 time to fit residues: 54.4175 Evaluate side-chains 251 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 166 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 33 TRP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 995 TYR Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 995 TYR Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1186 SER Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 467 CYS Chi-restraints excluded: chain C residue 779 ILE Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain C residue 1134 PHE Chi-restraints excluded: chain C residue 1186 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 221 optimal weight: 8.9990 chunk 140 optimal weight: 0.0050 chunk 176 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 208 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.091843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.054188 restraints weight = 56505.876| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.92 r_work: 0.2847 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18582 Z= 0.126 Angle : 0.561 8.533 25218 Z= 0.283 Chirality : 0.040 0.165 2826 Planarity : 0.003 0.044 3228 Dihedral : 3.791 26.264 2607 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.71 % Allowed : 26.93 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.18), residues: 2286 helix: 3.11 (0.33), residues: 255 sheet: 0.87 (0.20), residues: 735 loop : -1.29 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 13 TYR 0.010 0.001 TYR A 224 PHE 0.014 0.001 PHE A 347 TRP 0.017 0.001 TRP F 90 HIS 0.003 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00294 (18564) covalent geometry : angle 0.55965 (25179) SS BOND : bond 0.00297 ( 15) SS BOND : angle 1.06942 ( 30) hydrogen bonds : bond 0.04785 ( 671) hydrogen bonds : angle 4.11385 ( 2004) link_NAG-ASN : bond 0.00009 ( 3) link_NAG-ASN : angle 1.06858 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 176 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 67 LYS cc_start: 0.9088 (mmmm) cc_final: 0.8797 (mmmm) REVERT: A 271 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8289 (mttt) REVERT: A 779 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.8972 (mt) REVERT: A 1164 HIS cc_start: 0.9350 (m-70) cc_final: 0.8958 (m-70) REVERT: E 13 ARG cc_start: 0.8861 (mmm160) cc_final: 0.8476 (mmp-170) REVERT: E 67 LYS cc_start: 0.9201 (mmmm) cc_final: 0.8852 (mmmm) REVERT: E 104 ASP cc_start: 0.9285 (t0) cc_final: 0.9005 (t0) REVERT: E 116 VAL cc_start: 0.5678 (OUTLIER) cc_final: 0.5413 (p) REVERT: B 271 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8116 (mttt) REVERT: B 779 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.9058 (mt) REVERT: B 1164 HIS cc_start: 0.9378 (m-70) cc_final: 0.8989 (m-70) REVERT: G 23 LYS cc_start: 0.8594 (tppt) cc_final: 0.8386 (tppt) REVERT: G 67 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8892 (mmmm) REVERT: C 156 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8302 (t80) REVERT: C 271 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8286 (mptt) REVERT: C 337 MET cc_start: 0.8731 (mmm) cc_final: 0.8234 (mtt) REVERT: C 779 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9005 (mm) REVERT: C 1164 HIS cc_start: 0.9332 (m-70) cc_final: 0.8964 (m-70) outliers start: 92 outliers final: 73 residues processed: 256 average time/residue: 0.1342 time to fit residues: 53.8202 Evaluate side-chains 249 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 168 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 33 TRP Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 995 TYR Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 995 TYR Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1186 SER Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 467 CYS Chi-restraints excluded: chain C residue 779 ILE Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain C residue 1134 PHE Chi-restraints excluded: chain C residue 1229 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 95 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 222 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.092414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.054885 restraints weight = 56391.218| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.92 r_work: 0.2865 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18582 Z= 0.115 Angle : 0.567 9.118 25218 Z= 0.283 Chirality : 0.040 0.164 2826 Planarity : 0.003 0.049 3228 Dihedral : 3.647 24.126 2607 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.35 % Allowed : 27.44 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.18), residues: 2286 helix: 3.24 (0.34), residues: 255 sheet: 0.85 (0.20), residues: 741 loop : -1.23 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 13 TYR 0.010 0.001 TYR A 224 PHE 0.013 0.001 PHE A 347 TRP 0.014 0.001 TRP F 90 HIS 0.003 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00266 (18564) covalent geometry : angle 0.56624 (25179) SS BOND : bond 0.00291 ( 15) SS BOND : angle 0.97222 ( 30) hydrogen bonds : bond 0.04472 ( 671) hydrogen bonds : angle 4.03015 ( 2004) link_NAG-ASN : bond 0.00081 ( 3) link_NAG-ASN : angle 1.01007 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 173 time to evaluate : 0.435 Fit side-chains REVERT: D 67 LYS cc_start: 0.9081 (mmmm) cc_final: 0.8798 (mmmm) REVERT: A 779 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8957 (mt) REVERT: A 1164 HIS cc_start: 0.9350 (m-70) cc_final: 0.8951 (m-70) REVERT: E 13 ARG cc_start: 0.8902 (mmm160) cc_final: 0.8584 (mmp-170) REVERT: E 67 LYS cc_start: 0.9176 (mmmm) cc_final: 0.8851 (mmmm) REVERT: E 104 ASP cc_start: 0.9301 (t0) cc_final: 0.9025 (t0) REVERT: B 271 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8105 (mttt) REVERT: B 779 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9036 (mt) REVERT: B 1164 HIS cc_start: 0.9381 (m-70) cc_final: 0.9018 (m-70) REVERT: G 13 ARG cc_start: 0.8734 (mmm160) cc_final: 0.8512 (mmm160) REVERT: G 23 LYS cc_start: 0.8608 (tppt) cc_final: 0.8378 (tppt) REVERT: G 67 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8900 (mmmm) REVERT: C 156 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8432 (t80) REVERT: C 337 MET cc_start: 0.8723 (mmm) cc_final: 0.8290 (mtt) REVERT: C 779 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.8982 (mm) REVERT: C 1164 HIS cc_start: 0.9328 (m-70) cc_final: 0.8952 (m-70) outliers start: 85 outliers final: 76 residues processed: 246 average time/residue: 0.1114 time to fit residues: 43.1241 Evaluate side-chains 248 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 167 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 33 TRP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 995 TYR Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 995 TYR Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1186 SER Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 467 CYS Chi-restraints excluded: chain C residue 779 ILE Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain C residue 1134 PHE Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 1186 SER Chi-restraints excluded: chain C residue 1229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 156 optimal weight: 9.9990 chunk 182 optimal weight: 0.9990 chunk 187 optimal weight: 20.0000 chunk 134 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.091745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.054048 restraints weight = 56354.930| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.91 r_work: 0.2845 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18582 Z= 0.144 Angle : 0.587 9.071 25218 Z= 0.294 Chirality : 0.041 0.179 2826 Planarity : 0.003 0.038 3228 Dihedral : 3.729 24.523 2607 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.40 % Allowed : 27.44 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.18), residues: 2286 helix: 3.19 (0.33), residues: 255 sheet: 0.91 (0.19), residues: 762 loop : -1.28 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 13 TYR 0.011 0.001 TYR A 224 PHE 0.015 0.001 PHE A 347 TRP 0.019 0.001 TRP H 90 HIS 0.003 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00342 (18564) covalent geometry : angle 0.58606 (25179) SS BOND : bond 0.00310 ( 15) SS BOND : angle 1.09955 ( 30) hydrogen bonds : bond 0.04833 ( 671) hydrogen bonds : angle 4.06948 ( 2004) link_NAG-ASN : bond 0.00010 ( 3) link_NAG-ASN : angle 1.11811 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 170 time to evaluate : 0.562 Fit side-chains REVERT: D 67 LYS cc_start: 0.9102 (mmmm) cc_final: 0.8794 (mmmm) REVERT: A 779 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.8993 (mt) REVERT: A 1164 HIS cc_start: 0.9361 (m-70) cc_final: 0.8962 (m-70) REVERT: E 13 ARG cc_start: 0.8929 (mmm160) cc_final: 0.8627 (mmp-170) REVERT: E 67 LYS cc_start: 0.9181 (mmmm) cc_final: 0.8855 (mmmm) REVERT: E 104 ASP cc_start: 0.9294 (t0) cc_final: 0.9027 (t0) REVERT: B 271 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8106 (mttt) REVERT: B 779 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9063 (mt) REVERT: B 1164 HIS cc_start: 0.9394 (m-70) cc_final: 0.8999 (m-70) REVERT: G 13 ARG cc_start: 0.8827 (mmm160) cc_final: 0.8416 (mmp80) REVERT: G 23 LYS cc_start: 0.8590 (tppt) cc_final: 0.8372 (tppt) REVERT: G 67 LYS cc_start: 0.9212 (mmmm) cc_final: 0.8910 (mmmm) REVERT: C 156 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8431 (t80) REVERT: C 337 MET cc_start: 0.8746 (mmm) cc_final: 0.8302 (mtt) REVERT: C 779 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9018 (mm) REVERT: C 1164 HIS cc_start: 0.9341 (m-70) cc_final: 0.8970 (m-70) outliers start: 86 outliers final: 79 residues processed: 246 average time/residue: 0.1102 time to fit residues: 42.7730 Evaluate side-chains 251 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 167 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 33 TRP Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 995 TYR Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 995 TYR Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1186 SER Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 467 CYS Chi-restraints excluded: chain C residue 779 ILE Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain C residue 1134 PHE Chi-restraints excluded: chain C residue 1186 SER Chi-restraints excluded: chain C residue 1229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 25 optimal weight: 0.7980 chunk 159 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 chunk 179 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.091973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.054340 restraints weight = 56629.140| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.91 r_work: 0.2850 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18582 Z= 0.135 Angle : 0.578 8.800 25218 Z= 0.289 Chirality : 0.041 0.177 2826 Planarity : 0.003 0.038 3228 Dihedral : 3.675 23.820 2607 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.40 % Allowed : 27.34 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.18), residues: 2286 helix: 3.20 (0.33), residues: 255 sheet: 0.84 (0.20), residues: 747 loop : -1.21 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 13 TYR 0.010 0.001 TYR E 103 PHE 0.014 0.001 PHE A 347 TRP 0.017 0.001 TRP H 90 HIS 0.003 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00319 (18564) covalent geometry : angle 0.57664 (25179) SS BOND : bond 0.00311 ( 15) SS BOND : angle 1.06380 ( 30) hydrogen bonds : bond 0.04689 ( 671) hydrogen bonds : angle 4.04534 ( 2004) link_NAG-ASN : bond 0.00010 ( 3) link_NAG-ASN : angle 1.09774 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5166.84 seconds wall clock time: 89 minutes 16.03 seconds (5356.03 seconds total)