Starting phenix.real_space_refine on Sun Aug 24 23:10:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aa3_15292/08_2025/8aa3_15292.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aa3_15292/08_2025/8aa3_15292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aa3_15292/08_2025/8aa3_15292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aa3_15292/08_2025/8aa3_15292.map" model { file = "/net/cci-nas-00/data/ceres_data/8aa3_15292/08_2025/8aa3_15292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aa3_15292/08_2025/8aa3_15292.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 4 5.21 5 S 82 5.16 5 C 14914 2.51 5 N 3968 2.21 5 O 4666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23634 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4432 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 7260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7260 Classifications: {'peptide': 924} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 32, 'TRANS': 891} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4432 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 7260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7260 Classifications: {'peptide': 924} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 32, 'TRANS': 891} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FRU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FRU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 78 Unusual residues: {'FRU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 78 Unusual residues: {'FRU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.62, per 1000 atoms: 0.24 Number of scatterers: 23634 At special positions: 0 Unit cell: (109.695, 156.555, 135.255, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 Mg 4 11.99 O 4666 8.00 N 3968 7.00 C 14914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 389 " distance=2.03 Simple disulfide: pdb=" SG CYS J 387 " - pdb=" SG CYS J 389 " 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 ALPHA2-1 " FRU C 2 " - " FRU C 7 " ~> Even though FRU is a beta isomer, an alpha linkage is required... " FRU K 2 " - " FRU K 7 " ALPHA2-6 " FRU C 1 " - " FRU C 2 " " FRU C 2 " - " FRU C 3 " " FRU C 3 " - " FRU C 4 " " FRU C 4 " - " FRU C 5 " " FRU C 5 " - " FRU C 6 " " FRU D 1 " - " FRU D 2 " " FRU D 2 " - " FRU D 3 " " FRU D 3 " - " FRU D 4 " " FRU K 1 " - " FRU K 2 " " FRU K 2 " - " FRU K 3 " " FRU K 3 " - " FRU K 4 " " FRU K 4 " - " FRU K 5 " " FRU K 5 " - " FRU K 6 " " FRU L 1 " - " FRU L 2 " " FRU L 2 " - " FRU L 3 " " FRU L 3 " - " FRU L 4 " Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5360 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 28 sheets defined 27.5% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'B' and resid 24 through 39 removed outlier: 4.722A pdb=" N TRP B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.842A pdb=" N VAL B 53 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 54 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 77 Processing helix chain 'B' and resid 84 through 110 removed outlier: 3.868A pdb=" N GLN B 110 " --> pdb=" O GLN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 141 Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 166 through 185 removed outlier: 3.886A pdb=" N ASP B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 213 removed outlier: 3.720A pdb=" N TYR B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 238 through 245 removed outlier: 3.572A pdb=" N MET B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 245 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.883A pdb=" N LEU B 258 " --> pdb=" O MET B 255 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.501A pdb=" N GLU B 262 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 292 removed outlier: 4.737A pdb=" N LEU B 290 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 292 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 305 through 312 removed outlier: 3.559A pdb=" N VAL B 309 " --> pdb=" O SER B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.516A pdb=" N PHE B 342 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 422 removed outlier: 3.610A pdb=" N ASN B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 449 through 454 Processing helix chain 'B' and resid 469 through 485 Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 500 through 514 removed outlier: 4.303A pdb=" N SER B 514 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 removed outlier: 3.662A pdb=" N TYR B 519 " --> pdb=" O CYS B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 542 Processing helix chain 'A' and resid 105 through 112 removed outlier: 3.717A pdb=" N GLN A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.927A pdb=" N GLU A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 190 removed outlier: 4.643A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.543A pdb=" N ASN A 255 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA A 256 " --> pdb=" O ASN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 409 through 418 Processing helix chain 'A' and resid 535 through 539 Processing helix chain 'A' and resid 602 through 608 removed outlier: 5.721A pdb=" N ASN A 605 " --> pdb=" O THR A 602 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE A 606 " --> pdb=" O GLN A 603 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET A 607 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 608 " --> pdb=" O ASN A 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 602 through 608' Processing helix chain 'A' and resid 779 through 786 Processing helix chain 'A' and resid 815 through 822 Processing helix chain 'A' and resid 888 through 893 removed outlier: 3.898A pdb=" N LYS A 892 " --> pdb=" O SER A 888 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 893 " --> pdb=" O ASP A 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 888 through 893' Processing helix chain 'A' and resid 908 through 913 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 961 through 968 Processing helix chain 'J' and resid 24 through 39 removed outlier: 4.722A pdb=" N TRP J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA J 37 " --> pdb=" O TYR J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 55 removed outlier: 3.843A pdb=" N VAL J 53 " --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG J 54 " --> pdb=" O TYR J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 77 Processing helix chain 'J' and resid 84 through 110 removed outlier: 3.869A pdb=" N GLN J 110 " --> pdb=" O GLN J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 141 Processing helix chain 'J' and resid 154 through 160 Processing helix chain 'J' and resid 166 through 185 removed outlier: 3.886A pdb=" N ASP J 177 " --> pdb=" O LYS J 173 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE J 178 " --> pdb=" O ILE J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 213 removed outlier: 3.720A pdb=" N TYR J 213 " --> pdb=" O LEU J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 237 Processing helix chain 'J' and resid 238 through 245 removed outlier: 3.572A pdb=" N MET J 242 " --> pdb=" O ASP J 238 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY J 245 " --> pdb=" O ILE J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 262 removed outlier: 3.884A pdb=" N LEU J 258 " --> pdb=" O MET J 255 " (cutoff:3.500A) Proline residue: J 259 - end of helix removed outlier: 3.502A pdb=" N GLU J 262 " --> pdb=" O PRO J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 292 removed outlier: 4.737A pdb=" N LEU J 290 " --> pdb=" O GLY J 287 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR J 292 " --> pdb=" O GLY J 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 297 Processing helix chain 'J' and resid 305 through 312 removed outlier: 3.559A pdb=" N VAL J 309 " --> pdb=" O SER J 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 343 removed outlier: 3.516A pdb=" N PHE J 342 " --> pdb=" O PRO J 339 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 422 removed outlier: 3.609A pdb=" N ASN J 422 " --> pdb=" O LEU J 418 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 442 Processing helix chain 'J' and resid 449 through 454 Processing helix chain 'J' and resid 469 through 485 Processing helix chain 'J' and resid 490 through 499 Processing helix chain 'J' and resid 500 through 514 removed outlier: 4.304A pdb=" N SER J 514 " --> pdb=" O VAL J 510 " (cutoff:3.500A) Processing helix chain 'J' and resid 516 through 520 removed outlier: 3.662A pdb=" N TYR J 519 " --> pdb=" O CYS J 516 " (cutoff:3.500A) Processing helix chain 'J' and resid 535 through 542 Processing helix chain 'I' and resid 105 through 112 removed outlier: 3.717A pdb=" N GLN I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 121 Processing helix chain 'I' and resid 167 through 171 removed outlier: 3.926A pdb=" N GLU I 170 " --> pdb=" O GLY I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 removed outlier: 4.643A pdb=" N ILE I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 249 Processing helix chain 'I' and resid 251 through 256 removed outlier: 3.543A pdb=" N ASN I 255 " --> pdb=" O PRO I 252 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA I 256 " --> pdb=" O ASN I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 300 Processing helix chain 'I' and resid 376 through 384 Processing helix chain 'I' and resid 409 through 418 Processing helix chain 'I' and resid 535 through 539 Processing helix chain 'I' and resid 602 through 608 removed outlier: 5.721A pdb=" N ASN I 605 " --> pdb=" O THR I 602 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE I 606 " --> pdb=" O GLN I 603 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET I 607 " --> pdb=" O GLU I 604 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS I 608 " --> pdb=" O ASN I 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 602 through 608' Processing helix chain 'I' and resid 779 through 786 Processing helix chain 'I' and resid 815 through 822 Processing helix chain 'I' and resid 888 through 893 removed outlier: 3.898A pdb=" N LYS I 892 " --> pdb=" O SER I 888 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS I 893 " --> pdb=" O ASP I 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 888 through 893' Processing helix chain 'I' and resid 908 through 913 Processing helix chain 'I' and resid 939 through 941 No H-bonds generated for 'chain 'I' and resid 939 through 941' Processing helix chain 'I' and resid 961 through 968 Processing sheet with id=AA1, first strand: chain 'B' and resid 267 through 271 removed outlier: 7.356A pdb=" N SER B 267 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ARG B 406 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TRP B 269 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS B 402 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 3.782A pdb=" N ASN B 336 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 345 through 346 Processing sheet with id=AA4, first strand: chain 'B' and resid 390 through 392 Processing sheet with id=AA5, first strand: chain 'A' and resid 101 through 104 removed outlier: 4.014A pdb=" N ILE A 179 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 178 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 156 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE A 202 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE A 158 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N THR A 204 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA7, first strand: chain 'A' and resid 984 through 986 removed outlier: 3.896A pdb=" N VAL A 304 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG A 421 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG A 457 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N THR A 591 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLY A 626 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA A 740 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN A 953 " --> pdb=" O PHE A 877 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLN A 879 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU A 951 " --> pdb=" O GLN A 879 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL A 881 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU A 949 " --> pdb=" O VAL A 881 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 265 removed outlier: 6.595A pdb=" N ALA A 260 " --> pdb=" O MET A 276 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET A 276 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN A 262 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AB1, first strand: chain 'A' and resid 638 through 640 removed outlier: 6.396A pdb=" N ILE A 638 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AB3, first strand: chain 'A' and resid 804 through 806 removed outlier: 6.427A pdb=" N GLN A 804 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.918A pdb=" N ARG A 834 " --> pdb=" O ASP A 810 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AB6, first strand: chain 'J' and resid 267 through 271 removed outlier: 7.356A pdb=" N SER J 267 " --> pdb=" O ARG J 406 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ARG J 406 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TRP J 269 " --> pdb=" O VAL J 404 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS J 402 " --> pdb=" O ILE J 271 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 313 through 314 removed outlier: 3.783A pdb=" N ASN J 336 " --> pdb=" O THR J 314 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 345 through 346 Processing sheet with id=AB9, first strand: chain 'J' and resid 390 through 392 Processing sheet with id=AC1, first strand: chain 'I' and resid 101 through 104 removed outlier: 4.014A pdb=" N ILE I 179 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER I 178 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU I 156 " --> pdb=" O ILE I 200 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE I 202 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE I 158 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR I 204 " --> pdb=" O ILE I 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 128 through 131 Processing sheet with id=AC3, first strand: chain 'I' and resid 984 through 986 removed outlier: 3.896A pdb=" N VAL I 304 " --> pdb=" O LEU I 331 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG I 421 " --> pdb=" O ARG I 457 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG I 457 " --> pdb=" O ARG I 421 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N THR I 591 " --> pdb=" O GLY I 626 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLY I 626 " --> pdb=" O THR I 591 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA I 740 " --> pdb=" O LEU I 776 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN I 953 " --> pdb=" O PHE I 877 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLN I 879 " --> pdb=" O LEU I 951 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LEU I 951 " --> pdb=" O GLN I 879 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL I 881 " --> pdb=" O LEU I 949 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU I 949 " --> pdb=" O VAL I 881 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 259 through 265 removed outlier: 6.595A pdb=" N ALA I 260 " --> pdb=" O MET I 276 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET I 276 " --> pdb=" O ALA I 260 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN I 262 " --> pdb=" O TYR I 274 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 464 through 465 Processing sheet with id=AC6, first strand: chain 'I' and resid 638 through 640 removed outlier: 6.396A pdb=" N ILE I 638 " --> pdb=" O ASN I 676 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 719 through 722 Processing sheet with id=AC8, first strand: chain 'I' and resid 804 through 806 removed outlier: 6.427A pdb=" N GLN I 804 " --> pdb=" O ILE I 852 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 809 through 812 removed outlier: 4.918A pdb=" N ARG I 834 " --> pdb=" O ASP I 810 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 885 through 887 1096 hydrogen bonds defined for protein. 3042 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: 5.46 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7774 1.34 - 1.46: 6061 1.46 - 1.58: 10139 1.58 - 1.70: 66 1.70 - 1.82: 148 Bond restraints: 24188 Sorted by residual: bond pdb=" C2 FRU K 5 " pdb=" O5 FRU K 5 " ideal model delta sigma weight residual 1.412 1.642 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2 FRU C 4 " pdb=" O5 FRU C 4 " ideal model delta sigma weight residual 1.412 1.642 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2 FRU C 2 " pdb=" O5 FRU C 2 " ideal model delta sigma weight residual 1.412 1.642 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2 FRU K 4 " pdb=" O5 FRU K 4 " ideal model delta sigma weight residual 1.412 1.642 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2 FRU K 2 " pdb=" O5 FRU K 2 " ideal model delta sigma weight residual 1.412 1.642 -0.230 2.00e-02 2.50e+03 1.32e+02 ... (remaining 24183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 32402 1.73 - 3.47: 281 3.47 - 5.20: 85 5.20 - 6.94: 40 6.94 - 8.67: 2 Bond angle restraints: 32810 Sorted by residual: angle pdb=" C GLY B 393 " pdb=" N SER B 394 " pdb=" CA SER B 394 " ideal model delta sigma weight residual 121.54 127.55 -6.01 1.91e+00 2.74e-01 9.90e+00 angle pdb=" C GLY J 393 " pdb=" N SER J 394 " pdb=" CA SER J 394 " ideal model delta sigma weight residual 121.54 127.54 -6.00 1.91e+00 2.74e-01 9.88e+00 angle pdb=" C ILE I 353 " pdb=" N ASP I 354 " pdb=" CA ASP I 354 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.66e+00 angle pdb=" C ILE A 353 " pdb=" N ASP A 354 " pdb=" CA ASP A 354 " ideal model delta sigma weight residual 121.54 127.11 -5.57 1.91e+00 2.74e-01 8.50e+00 angle pdb=" CA LEU A 121 " pdb=" CB LEU A 121 " pdb=" CG LEU A 121 " ideal model delta sigma weight residual 116.30 124.97 -8.67 3.50e+00 8.16e-02 6.14e+00 ... (remaining 32805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 13088 17.71 - 35.42: 1074 35.42 - 53.13: 230 53.13 - 70.84: 70 70.84 - 88.56: 20 Dihedral angle restraints: 14482 sinusoidal: 5990 harmonic: 8492 Sorted by residual: dihedral pdb=" CB CYS B 387 " pdb=" SG CYS B 387 " pdb=" SG CYS B 389 " pdb=" CB CYS B 389 " ideal model delta sinusoidal sigma weight residual 93.00 124.13 -31.13 1 1.00e+01 1.00e-02 1.38e+01 dihedral pdb=" CB CYS J 387 " pdb=" SG CYS J 387 " pdb=" SG CYS J 389 " pdb=" CB CYS J 389 " ideal model delta sinusoidal sigma weight residual 93.00 124.11 -31.11 1 1.00e+01 1.00e-02 1.38e+01 dihedral pdb=" CG ARG A 444 " pdb=" CD ARG A 444 " pdb=" NE ARG A 444 " pdb=" CZ ARG A 444 " ideal model delta sinusoidal sigma weight residual -180.00 -136.01 -43.99 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 14479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2095 0.030 - 0.060: 950 0.060 - 0.091: 230 0.091 - 0.121: 162 0.121 - 0.151: 37 Chirality restraints: 3474 Sorted by residual: chirality pdb=" C2 FRU K 7 " pdb=" O1 FRU K 2 " pdb=" C1 FRU K 7 " pdb=" O5 FRU K 7 " both_signs ideal model delta sigma weight residual False 2.60 2.75 -0.15 2.00e-02 2.50e+03 5.43e+01 chirality pdb=" C2 FRU C 7 " pdb=" O1 FRU C 2 " pdb=" C1 FRU C 7 " pdb=" O5 FRU C 7 " both_signs ideal model delta sigma weight residual False 2.60 2.74 -0.14 2.00e-02 2.50e+03 5.21e+01 chirality pdb=" C2 FRU K 3 " pdb=" O6 FRU K 2 " pdb=" C1 FRU K 3 " pdb=" O5 FRU K 3 " both_signs ideal model delta sigma weight residual False 2.60 2.68 -0.08 2.00e-02 2.50e+03 1.57e+01 ... (remaining 3471 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 530 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO I 531 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO I 531 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO I 531 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 530 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 531 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 531 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 531 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 353 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C ILE A 353 " -0.020 2.00e-02 2.50e+03 pdb=" O ILE A 353 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP A 354 " 0.007 2.00e-02 2.50e+03 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 322 2.65 - 3.21: 20933 3.21 - 3.77: 37958 3.77 - 4.34: 54363 4.34 - 4.90: 90061 Nonbonded interactions: 203637 Sorted by model distance: nonbonded pdb=" OD1 ASN J 401 " pdb="MG MG J 601 " model vdw 2.085 2.170 nonbonded pdb=" OD1 ASN B 401 " pdb="MG MG B 601 " model vdw 2.086 2.170 nonbonded pdb=" OD1 ASN I 841 " pdb="MG MG I1101 " model vdw 2.131 2.170 nonbonded pdb=" OD1 ASN A 841 " pdb="MG MG A1101 " model vdw 2.132 2.170 nonbonded pdb=" O TYR B 273 " pdb="MG MG B 601 " model vdw 2.144 2.170 ... (remaining 203632 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 'B' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 24.110 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 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 : 0.011 0.230 24208 Z= 0.536 Angle : 0.525 8.671 32868 Z= 0.243 Chirality : 0.042 0.151 3474 Planarity : 0.003 0.032 4272 Dihedral : 14.247 88.556 9116 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % 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 aren not related in a simple way. whole: 1.42 (0.16), residues: 2942 helix: 1.72 (0.20), residues: 690 sheet: 1.05 (0.17), residues: 820 loop : 0.62 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 408 TYR 0.011 0.001 TYR B 95 PHE 0.008 0.001 PHE A 758 TRP 0.013 0.001 TRP B 91 HIS 0.002 0.000 HIS A 799 Details of bonding type rmsd covalent geometry : bond 0.01049 (24188) covalent geometry : angle 0.50373 (32810) SS BOND : bond 0.00270 ( 2) SS BOND : angle 0.41495 ( 4) hydrogen bonds : bond 0.11477 ( 1096) hydrogen bonds : angle 4.92385 ( 3042) glycosidic custom : bond 0.04101 ( 2) glycosidic custom : angle 3.57713 ( 6) link_ALPHA2-6 : bond 0.08215 ( 16) link_ALPHA2-6 : angle 3.67020 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.930 Fit side-chains REVERT: B 18 GLN cc_start: 0.8670 (mt0) cc_final: 0.8327 (mt0) REVERT: J 18 GLN cc_start: 0.8664 (mt0) cc_final: 0.8318 (mt0) REVERT: I 988 LYS cc_start: 0.8490 (mppt) cc_final: 0.8186 (mppt) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.7682 time to fit residues: 172.1602 Evaluate side-chains 116 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 96 GLN B 167 ASN B 220 ASN A 153 ASN A 677 GLN A 767 ASN A 816 GLN J 43 ASN J 96 GLN J 167 ASN J 220 ASN I 153 ASN I 211 GLN I 677 GLN I 767 ASN I 816 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.081663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.067739 restraints weight = 41882.661| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.87 r_work: 0.2861 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24208 Z= 0.155 Angle : 0.515 6.335 32868 Z= 0.265 Chirality : 0.043 0.160 3474 Planarity : 0.003 0.034 4272 Dihedral : 7.599 54.608 3714 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.50 % Allowed : 5.34 % Favored : 93.17 % 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 aren not related in a simple way. whole: 1.32 (0.16), residues: 2942 helix: 1.59 (0.21), residues: 674 sheet: 1.04 (0.17), residues: 808 loop : 0.57 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 100 TYR 0.013 0.001 TYR J 95 PHE 0.010 0.001 PHE B 342 TRP 0.009 0.001 TRP B 91 HIS 0.003 0.001 HIS J 132 Details of bonding type rmsd covalent geometry : bond 0.00350 (24188) covalent geometry : angle 0.49644 (32810) SS BOND : bond 0.00198 ( 2) SS BOND : angle 0.61346 ( 4) hydrogen bonds : bond 0.03759 ( 1096) hydrogen bonds : angle 4.34462 ( 3042) glycosidic custom : bond 0.00213 ( 2) glycosidic custom : angle 3.66736 ( 6) link_ALPHA2-6 : bond 0.01186 ( 16) link_ALPHA2-6 : angle 3.34963 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.871 Fit side-chains REVERT: B 18 GLN cc_start: 0.8885 (mt0) cc_final: 0.8573 (mt0) REVERT: A 502 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7759 (mtp-110) REVERT: A 561 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7607 (tmt) REVERT: A 709 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8120 (mm-30) REVERT: A 988 LYS cc_start: 0.8736 (mppt) cc_final: 0.8333 (mppt) REVERT: J 18 GLN cc_start: 0.8873 (mt0) cc_final: 0.8565 (mt0) REVERT: I 561 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7650 (tmt) REVERT: I 709 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8130 (mm-30) REVERT: I 741 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8896 (mtp) REVERT: I 988 LYS cc_start: 0.8732 (mppt) cc_final: 0.8329 (mppt) outliers start: 37 outliers final: 11 residues processed: 142 average time/residue: 0.7981 time to fit residues: 128.4744 Evaluate side-chains 122 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 594 SER Chi-restraints excluded: chain I residue 709 GLU Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 769 SER Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 909 THR Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 16 optimal weight: 4.9990 chunk 287 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 279 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 197 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 ASN A 362 HIS J 283 ASN I 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.077559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.063180 restraints weight = 41631.832| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.88 r_work: 0.2754 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24208 Z= 0.189 Angle : 0.513 12.077 32868 Z= 0.271 Chirality : 0.043 0.162 3474 Planarity : 0.004 0.046 4272 Dihedral : 6.273 47.924 3714 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.46 % Allowed : 6.83 % Favored : 91.71 % 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 aren not related in a simple way. whole: 1.06 (0.15), residues: 2942 helix: 1.33 (0.20), residues: 684 sheet: 0.94 (0.17), residues: 826 loop : 0.38 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 100 TYR 0.014 0.001 TYR A 422 PHE 0.011 0.001 PHE B 71 TRP 0.010 0.001 TRP J 91 HIS 0.004 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00431 (24188) covalent geometry : angle 0.50377 (32810) SS BOND : bond 0.00252 ( 2) SS BOND : angle 0.93144 ( 4) hydrogen bonds : bond 0.04184 ( 1096) hydrogen bonds : angle 4.53651 ( 3042) glycosidic custom : bond 0.01740 ( 2) glycosidic custom : angle 2.25932 ( 6) link_ALPHA2-6 : bond 0.01474 ( 16) link_ALPHA2-6 : angle 2.46947 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 1.009 Fit side-chains REVERT: B 18 GLN cc_start: 0.8874 (mt0) cc_final: 0.8534 (mt0) REVERT: B 203 TYR cc_start: 0.9418 (OUTLIER) cc_final: 0.8693 (t80) REVERT: A 502 ARG cc_start: 0.8131 (ttm110) cc_final: 0.7808 (mtp-110) REVERT: A 561 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7723 (tmt) REVERT: A 709 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8126 (mm-30) REVERT: A 988 LYS cc_start: 0.8721 (mppt) cc_final: 0.8317 (mppt) REVERT: J 18 GLN cc_start: 0.8864 (mt0) cc_final: 0.8516 (mt0) REVERT: J 203 TYR cc_start: 0.9421 (OUTLIER) cc_final: 0.8696 (t80) REVERT: I 502 ARG cc_start: 0.8253 (mtp-110) cc_final: 0.7890 (mtm-85) REVERT: I 561 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7748 (tmt) REVERT: I 709 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8133 (mm-30) REVERT: I 988 LYS cc_start: 0.8728 (mppt) cc_final: 0.8324 (mppt) outliers start: 36 outliers final: 13 residues processed: 142 average time/residue: 0.7697 time to fit residues: 124.7415 Evaluate side-chains 129 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 594 SER Chi-restraints excluded: chain I residue 709 GLU Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 769 SER Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 909 THR Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 1 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 276 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 224 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN A 702 GLN A 767 ASN I 489 ASN I 677 GLN I 702 GLN I 767 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.073827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.058797 restraints weight = 40932.936| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 1.92 r_work: 0.2595 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 24208 Z= 0.241 Angle : 0.556 11.416 32868 Z= 0.294 Chirality : 0.045 0.153 3474 Planarity : 0.004 0.058 4272 Dihedral : 5.949 50.088 3714 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.86 % Allowed : 7.84 % Favored : 90.30 % 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 aren not related in a simple way. whole: 0.83 (0.15), residues: 2942 helix: 1.09 (0.20), residues: 676 sheet: 0.90 (0.17), residues: 826 loop : 0.21 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 100 TYR 0.015 0.001 TYR A1002 PHE 0.011 0.002 PHE B 71 TRP 0.012 0.001 TRP I 486 HIS 0.004 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00555 (24188) covalent geometry : angle 0.54392 (32810) SS BOND : bond 0.00261 ( 2) SS BOND : angle 1.09301 ( 4) hydrogen bonds : bond 0.04552 ( 1096) hydrogen bonds : angle 4.73560 ( 3042) glycosidic custom : bond 0.01028 ( 2) glycosidic custom : angle 2.85986 ( 6) link_ALPHA2-6 : bond 0.01109 ( 16) link_ALPHA2-6 : angle 2.86772 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 113 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: B 18 GLN cc_start: 0.8822 (mt0) cc_final: 0.8176 (mt0) REVERT: B 203 TYR cc_start: 0.9451 (OUTLIER) cc_final: 0.8718 (t80) REVERT: A 561 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7778 (tmt) REVERT: A 709 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: A 741 MET cc_start: 0.9131 (mtp) cc_final: 0.8894 (ttp) REVERT: A 988 LYS cc_start: 0.8771 (mppt) cc_final: 0.8321 (mppt) REVERT: J 18 GLN cc_start: 0.8817 (mt0) cc_final: 0.8172 (mt0) REVERT: J 203 TYR cc_start: 0.9445 (OUTLIER) cc_final: 0.8704 (t80) REVERT: I 502 ARG cc_start: 0.8336 (mtp-110) cc_final: 0.7981 (mtm-85) REVERT: I 561 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7848 (tmt) REVERT: I 709 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8118 (mm-30) REVERT: I 988 LYS cc_start: 0.8771 (mppt) cc_final: 0.8324 (mppt) outliers start: 46 outliers final: 17 residues processed: 141 average time/residue: 0.7647 time to fit residues: 123.5067 Evaluate side-chains 136 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 427 MET Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 594 SER Chi-restraints excluded: chain I residue 709 GLU Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 769 SER Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 909 THR Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 183 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 GLN A 767 ASN I 767 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.072355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.057356 restraints weight = 41121.116| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 1.90 r_work: 0.2563 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2423 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 24208 Z= 0.330 Angle : 0.606 14.047 32868 Z= 0.320 Chirality : 0.047 0.161 3474 Planarity : 0.004 0.067 4272 Dihedral : 6.182 51.968 3714 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.78 % Allowed : 8.53 % Favored : 89.69 % 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 aren not related in a simple way. whole: 0.64 (0.15), residues: 2942 helix: 0.84 (0.20), residues: 674 sheet: 0.95 (0.18), residues: 806 loop : 0.02 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 100 TYR 0.016 0.002 TYR I1002 PHE 0.013 0.002 PHE J 71 TRP 0.013 0.002 TRP J 91 HIS 0.005 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00768 (24188) covalent geometry : angle 0.59542 (32810) SS BOND : bond 0.00376 ( 2) SS BOND : angle 1.46588 ( 4) hydrogen bonds : bond 0.04946 ( 1096) hydrogen bonds : angle 4.96272 ( 3042) glycosidic custom : bond 0.01339 ( 2) glycosidic custom : angle 2.59775 ( 6) link_ALPHA2-6 : bond 0.01029 ( 16) link_ALPHA2-6 : angle 2.87158 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 0.853 Fit side-chains REVERT: B 18 GLN cc_start: 0.8847 (mt0) cc_final: 0.8189 (mt0) REVERT: B 203 TYR cc_start: 0.9495 (OUTLIER) cc_final: 0.8794 (t80) REVERT: A 561 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7774 (tmt) REVERT: A 988 LYS cc_start: 0.8792 (mppt) cc_final: 0.8354 (mppt) REVERT: J 18 GLN cc_start: 0.8838 (mt0) cc_final: 0.8187 (mt0) REVERT: J 203 TYR cc_start: 0.9484 (OUTLIER) cc_final: 0.8778 (t80) REVERT: I 502 ARG cc_start: 0.8367 (mtp-110) cc_final: 0.8020 (mtm-85) REVERT: I 561 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7799 (tmt) REVERT: I 988 LYS cc_start: 0.8774 (mppt) cc_final: 0.8345 (mppt) outliers start: 44 outliers final: 16 residues processed: 142 average time/residue: 0.8266 time to fit residues: 132.5590 Evaluate side-chains 133 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 594 SER Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 769 SER Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 909 THR Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 0.0020 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 259 optimal weight: 0.0000 chunk 198 optimal weight: 0.6980 chunk 152 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN A 366 ASN A 434 ASN A 586 ASN A 767 ASN J 96 GLN I 366 ASN I 434 ASN I 586 ASN I 767 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.078343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.064438 restraints weight = 41949.386| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.85 r_work: 0.2776 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24208 Z= 0.094 Angle : 0.469 11.152 32868 Z= 0.250 Chirality : 0.041 0.143 3474 Planarity : 0.003 0.030 4272 Dihedral : 5.269 49.596 3714 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.01 % Allowed : 9.82 % Favored : 89.17 % 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 aren not related in a simple way. whole: 0.83 (0.15), residues: 2942 helix: 1.12 (0.20), residues: 680 sheet: 0.96 (0.18), residues: 802 loop : 0.15 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 426 TYR 0.010 0.001 TYR J 95 PHE 0.011 0.001 PHE A 428 TRP 0.017 0.001 TRP J 91 HIS 0.002 0.001 HIS A 482 Details of bonding type rmsd covalent geometry : bond 0.00190 (24188) covalent geometry : angle 0.45694 (32810) SS BOND : bond 0.00296 ( 2) SS BOND : angle 0.87053 ( 4) hydrogen bonds : bond 0.03303 ( 1096) hydrogen bonds : angle 4.47623 ( 3042) glycosidic custom : bond 0.00886 ( 2) glycosidic custom : angle 2.88190 ( 6) link_ALPHA2-6 : bond 0.01236 ( 16) link_ALPHA2-6 : angle 2.65301 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.846 Fit side-chains REVERT: B 7 ARG cc_start: 0.7960 (ttp-170) cc_final: 0.7569 (ttm170) REVERT: B 18 GLN cc_start: 0.8753 (mt0) cc_final: 0.8407 (mt0) REVERT: B 203 TYR cc_start: 0.9327 (OUTLIER) cc_final: 0.8675 (t80) REVERT: A 502 ARG cc_start: 0.8315 (ttm170) cc_final: 0.8081 (ttm170) REVERT: A 506 MET cc_start: 0.8828 (ttt) cc_final: 0.8586 (ppp) REVERT: A 561 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7699 (tmt) REVERT: A 709 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8082 (mm-30) REVERT: A 876 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8405 (ttm) REVERT: A 988 LYS cc_start: 0.8852 (mppt) cc_final: 0.8516 (mppt) REVERT: J 7 ARG cc_start: 0.7999 (ttp-170) cc_final: 0.7567 (ttm170) REVERT: J 18 GLN cc_start: 0.8762 (mt0) cc_final: 0.8420 (mt0) REVERT: J 203 TYR cc_start: 0.9322 (OUTLIER) cc_final: 0.8666 (t80) REVERT: I 502 ARG cc_start: 0.8326 (mtp-110) cc_final: 0.7954 (mtm-85) REVERT: I 506 MET cc_start: 0.8824 (ttt) cc_final: 0.8600 (ppp) REVERT: I 561 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7778 (tmt) REVERT: I 709 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8089 (mm-30) REVERT: I 988 LYS cc_start: 0.8839 (mppt) cc_final: 0.8516 (mppt) outliers start: 25 outliers final: 4 residues processed: 135 average time/residue: 0.7231 time to fit residues: 110.6077 Evaluate side-chains 126 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 709 GLU Chi-restraints excluded: chain I residue 876 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 156 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 39 optimal weight: 0.0000 chunk 173 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 287 optimal weight: 1.9990 chunk 257 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN I 489 ASN I 749 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.075843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.060769 restraints weight = 40443.072| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 1.92 r_work: 0.2635 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 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 0.045 24208 Z= 0.138 Angle : 0.487 13.654 32868 Z= 0.258 Chirality : 0.042 0.145 3474 Planarity : 0.003 0.036 4272 Dihedral : 5.216 48.979 3714 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.09 % Allowed : 9.98 % Favored : 88.92 % 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 aren not related in a simple way. whole: 0.88 (0.15), residues: 2942 helix: 1.19 (0.20), residues: 680 sheet: 0.92 (0.18), residues: 806 loop : 0.21 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 100 TYR 0.013 0.001 TYR J 95 PHE 0.010 0.001 PHE A 606 TRP 0.012 0.001 TRP J 91 HIS 0.003 0.001 HIS J 132 Details of bonding type rmsd covalent geometry : bond 0.00311 (24188) covalent geometry : angle 0.47491 (32810) SS BOND : bond 0.00533 ( 2) SS BOND : angle 1.16194 ( 4) hydrogen bonds : bond 0.03604 ( 1096) hydrogen bonds : angle 4.48975 ( 3042) glycosidic custom : bond 0.00971 ( 2) glycosidic custom : angle 2.69140 ( 6) link_ALPHA2-6 : bond 0.01206 ( 16) link_ALPHA2-6 : angle 2.71573 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.788 Fit side-chains REVERT: B 7 ARG cc_start: 0.7996 (ttp-170) cc_final: 0.7579 (ttm170) REVERT: B 18 GLN cc_start: 0.8759 (mt0) cc_final: 0.8426 (mt0) REVERT: B 203 TYR cc_start: 0.9369 (OUTLIER) cc_final: 0.8580 (t80) REVERT: A 502 ARG cc_start: 0.8353 (ttm170) cc_final: 0.8114 (ttm170) REVERT: A 561 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7689 (tmt) REVERT: A 709 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8110 (mm-30) REVERT: A 988 LYS cc_start: 0.8819 (mppt) cc_final: 0.8474 (mppt) REVERT: J 7 ARG cc_start: 0.7986 (ttp-170) cc_final: 0.7538 (ttm170) REVERT: J 18 GLN cc_start: 0.8776 (mt0) cc_final: 0.8447 (mt0) REVERT: J 203 TYR cc_start: 0.9363 (OUTLIER) cc_final: 0.8568 (t80) REVERT: I 502 ARG cc_start: 0.8337 (mtp-110) cc_final: 0.7958 (mtm-85) REVERT: I 561 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7781 (tmt) REVERT: I 709 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8116 (mm-30) REVERT: I 988 LYS cc_start: 0.8817 (mppt) cc_final: 0.8480 (mppt) outliers start: 27 outliers final: 7 residues processed: 134 average time/residue: 0.6766 time to fit residues: 103.1725 Evaluate side-chains 126 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 709 GLU Chi-restraints excluded: chain I residue 876 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 121 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 286 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 189 optimal weight: 0.0050 chunk 220 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN A 749 ASN A 767 ASN I 489 ASN I 586 ASN I 767 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.075441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.060350 restraints weight = 40495.261| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 1.93 r_work: 0.2627 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24208 Z= 0.156 Angle : 0.495 10.987 32868 Z= 0.261 Chirality : 0.043 0.143 3474 Planarity : 0.003 0.037 4272 Dihedral : 5.235 49.938 3714 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.01 % Allowed : 10.27 % Favored : 88.72 % 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 aren not related in a simple way. whole: 0.85 (0.15), residues: 2942 helix: 1.18 (0.20), residues: 680 sheet: 0.90 (0.18), residues: 806 loop : 0.18 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 100 TYR 0.012 0.001 TYR I 422 PHE 0.010 0.001 PHE A 606 TRP 0.012 0.001 TRP J 91 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00355 (24188) covalent geometry : angle 0.48231 (32810) SS BOND : bond 0.00394 ( 2) SS BOND : angle 1.18985 ( 4) hydrogen bonds : bond 0.03743 ( 1096) hydrogen bonds : angle 4.51887 ( 3042) glycosidic custom : bond 0.01031 ( 2) glycosidic custom : angle 2.67166 ( 6) link_ALPHA2-6 : bond 0.01173 ( 16) link_ALPHA2-6 : angle 2.73006 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 1.071 Fit side-chains REVERT: B 7 ARG cc_start: 0.7994 (ttp-170) cc_final: 0.7565 (ttm170) REVERT: B 18 GLN cc_start: 0.8803 (mt0) cc_final: 0.8458 (mt0) REVERT: B 203 TYR cc_start: 0.9384 (OUTLIER) cc_final: 0.8601 (t80) REVERT: A 561 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7761 (tmt) REVERT: A 824 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.9180 (p) REVERT: A 988 LYS cc_start: 0.8809 (mppt) cc_final: 0.8469 (mppt) REVERT: J 7 ARG cc_start: 0.8010 (ttp-170) cc_final: 0.7555 (ttm170) REVERT: J 18 GLN cc_start: 0.8822 (mt0) cc_final: 0.8480 (mt0) REVERT: J 203 TYR cc_start: 0.9375 (OUTLIER) cc_final: 0.8589 (t80) REVERT: I 502 ARG cc_start: 0.8341 (mtp-110) cc_final: 0.7965 (mtm-85) REVERT: I 561 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7784 (tmt) REVERT: I 988 LYS cc_start: 0.8813 (mppt) cc_final: 0.8478 (mppt) outliers start: 25 outliers final: 8 residues processed: 129 average time/residue: 0.8113 time to fit residues: 118.4723 Evaluate side-chains 126 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 876 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 54 optimal weight: 2.9990 chunk 273 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 163 optimal weight: 0.2980 chunk 173 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN A 749 ASN I 489 ASN I 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.075089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.059999 restraints weight = 40599.869| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 1.92 r_work: 0.2618 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24208 Z= 0.169 Angle : 0.506 14.652 32868 Z= 0.267 Chirality : 0.043 0.164 3474 Planarity : 0.003 0.041 4272 Dihedral : 5.263 51.185 3714 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.81 % Allowed : 10.67 % Favored : 88.52 % 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 aren not related in a simple way. whole: 0.82 (0.15), residues: 2942 helix: 1.12 (0.20), residues: 680 sheet: 0.91 (0.18), residues: 806 loop : 0.16 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 100 TYR 0.013 0.001 TYR J 95 PHE 0.010 0.001 PHE B 342 TRP 0.012 0.001 TRP J 91 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00385 (24188) covalent geometry : angle 0.49426 (32810) SS BOND : bond 0.00454 ( 2) SS BOND : angle 1.19907 ( 4) hydrogen bonds : bond 0.03884 ( 1096) hydrogen bonds : angle 4.56316 ( 3042) glycosidic custom : bond 0.01040 ( 2) glycosidic custom : angle 2.65822 ( 6) link_ALPHA2-6 : bond 0.01154 ( 16) link_ALPHA2-6 : angle 2.74064 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.930 Fit side-chains REVERT: B 7 ARG cc_start: 0.8003 (ttp-170) cc_final: 0.7572 (ttm170) REVERT: B 18 GLN cc_start: 0.8804 (mt0) cc_final: 0.8465 (mt0) REVERT: B 203 TYR cc_start: 0.9402 (OUTLIER) cc_final: 0.8637 (t80) REVERT: A 502 ARG cc_start: 0.8395 (ttm110) cc_final: 0.8103 (ttm170) REVERT: A 561 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7762 (tmt) REVERT: A 824 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.9170 (p) REVERT: A 988 LYS cc_start: 0.8792 (mppt) cc_final: 0.8462 (mppt) REVERT: J 7 ARG cc_start: 0.8020 (ttp-170) cc_final: 0.7562 (ttm170) REVERT: J 18 GLN cc_start: 0.8821 (mt0) cc_final: 0.8486 (mt0) REVERT: J 203 TYR cc_start: 0.9394 (OUTLIER) cc_final: 0.8625 (t80) REVERT: I 502 ARG cc_start: 0.8350 (mtp-110) cc_final: 0.7972 (ttm170) REVERT: I 561 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7787 (tmt) REVERT: I 988 LYS cc_start: 0.8805 (mppt) cc_final: 0.8479 (mppt) outliers start: 20 outliers final: 7 residues processed: 128 average time/residue: 0.7856 time to fit residues: 113.9325 Evaluate side-chains 125 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 876 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 78 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 267 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 137 optimal weight: 0.4980 chunk 228 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN A 586 ASN I 489 ASN I 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.073663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.058579 restraints weight = 40867.499| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 1.92 r_work: 0.2586 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 24208 Z= 0.250 Angle : 0.558 13.336 32868 Z= 0.294 Chirality : 0.045 0.174 3474 Planarity : 0.004 0.056 4272 Dihedral : 5.556 53.109 3714 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.69 % Allowed : 10.87 % Favored : 88.44 % 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 aren not related in a simple way. whole: 0.71 (0.15), residues: 2942 helix: 0.99 (0.20), residues: 676 sheet: 0.86 (0.18), residues: 806 loop : 0.10 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 100 TYR 0.016 0.001 TYR I 422 PHE 0.011 0.002 PHE J 485 TRP 0.012 0.001 TRP J 36 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00579 (24188) covalent geometry : angle 0.54595 (32810) SS BOND : bond 0.00512 ( 2) SS BOND : angle 1.38763 ( 4) hydrogen bonds : bond 0.04409 ( 1096) hydrogen bonds : angle 4.74862 ( 3042) glycosidic custom : bond 0.01114 ( 2) glycosidic custom : angle 2.61405 ( 6) link_ALPHA2-6 : bond 0.01090 ( 16) link_ALPHA2-6 : angle 2.84799 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.837 Fit side-chains REVERT: B 7 ARG cc_start: 0.8088 (ttp-170) cc_final: 0.7657 (ttm170) REVERT: B 18 GLN cc_start: 0.8810 (mt0) cc_final: 0.8481 (mt0) REVERT: B 203 TYR cc_start: 0.9457 (OUTLIER) cc_final: 0.8735 (t80) REVERT: A 561 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7772 (tmt) REVERT: A 824 THR cc_start: 0.9420 (OUTLIER) cc_final: 0.9171 (p) REVERT: A 988 LYS cc_start: 0.8802 (mppt) cc_final: 0.8485 (mppt) REVERT: J 7 ARG cc_start: 0.8133 (ttp-170) cc_final: 0.7692 (ttm170) REVERT: J 18 GLN cc_start: 0.8822 (mt0) cc_final: 0.8499 (mt0) REVERT: J 203 TYR cc_start: 0.9440 (OUTLIER) cc_final: 0.8703 (t80) REVERT: I 502 ARG cc_start: 0.8358 (mtp-110) cc_final: 0.7976 (ttm170) REVERT: I 561 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7803 (tmt) REVERT: I 988 LYS cc_start: 0.8812 (mppt) cc_final: 0.8496 (mppt) outliers start: 17 outliers final: 8 residues processed: 123 average time/residue: 0.7904 time to fit residues: 110.1646 Evaluate side-chains 122 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 876 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 198 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 232 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 286 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 266 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 586 ASN A 767 ASN I 306 GLN I 586 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.075466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.060770 restraints weight = 40633.314| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 1.89 r_work: 0.2645 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24208 Z= 0.117 Angle : 0.478 11.284 32868 Z= 0.254 Chirality : 0.042 0.140 3474 Planarity : 0.003 0.031 4272 Dihedral : 5.154 52.901 3714 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.57 % Allowed : 10.95 % Favored : 88.48 % 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 aren not related in a simple way. whole: 0.80 (0.15), residues: 2942 helix: 1.09 (0.20), residues: 680 sheet: 0.91 (0.18), residues: 802 loop : 0.16 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 502 TYR 0.011 0.001 TYR A 422 PHE 0.010 0.001 PHE A 606 TRP 0.016 0.001 TRP B 91 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00254 (24188) covalent geometry : angle 0.46578 (32810) SS BOND : bond 0.00380 ( 2) SS BOND : angle 0.98120 ( 4) hydrogen bonds : bond 0.03525 ( 1096) hydrogen bonds : angle 4.51781 ( 3042) glycosidic custom : bond 0.00953 ( 2) glycosidic custom : angle 2.65327 ( 6) link_ALPHA2-6 : bond 0.01197 ( 16) link_ALPHA2-6 : angle 2.67701 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6460.56 seconds wall clock time: 111 minutes 41.02 seconds (6701.02 seconds total)