Starting phenix.real_space_refine on Fri May 23 01:33:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aa3_15292/05_2025/8aa3_15292.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aa3_15292/05_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_15292/05_2025/8aa3_15292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aa3_15292/05_2025/8aa3_15292.map" model { file = "/net/cci-nas-00/data/ceres_data/8aa3_15292/05_2025/8aa3_15292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aa3_15292/05_2025/8aa3_15292.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.12, per 1000 atoms: 0.60 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: 6.84 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 2.97 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: 9.42 Time building geometry restraints manager: 7.74 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: 0.11 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.980 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 54.930 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.110 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:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.250 ------------------------------------------------------------------------------- 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 : 7.26 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (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 TRP 0.013 0.001 TRP B 91 HIS 0.002 0.000 HIS A 799 PHE 0.008 0.001 PHE A 758 TYR 0.011 0.001 TYR B 95 ARG 0.003 0.000 ARG I 408 Details of bonding type rmsd link_ALPHA2-6 : bond 0.08215 ( 16) link_ALPHA2-6 : angle 3.67020 ( 48) hydrogen bonds : bond 0.11477 ( 1096) hydrogen bonds : angle 4.92385 ( 3042) SS BOND : bond 0.00270 ( 2) SS BOND : angle 0.41495 ( 4) glycosidic custom : bond 0.04101 ( 2) glycosidic custom : angle 3.57713 ( 6) covalent geometry : bond 0.01049 (24188) covalent geometry : angle 0.50373 (32810) *********************** 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 : 2.813 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: 1.4471 time to fit residues: 326.5650 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 : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 1.9990 chunk 222 optimal weight: 6.9990 chunk 123 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 230 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 140 optimal weight: 0.5980 chunk 171 optimal weight: 6.9990 chunk 266 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 677 GLN A 767 ASN A 816 GLN J 43 ASN J 96 GLN J 167 ASN J 220 ASN I 211 GLN I 642 ASN I 677 GLN I 749 ASN 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 = 0.3253 r_free = 0.3253 target = 0.082929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068972 restraints weight = 41387.404| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.88 r_work: 0.2898 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24208 Z= 0.123 Angle : 0.497 6.551 32868 Z= 0.255 Chirality : 0.042 0.162 3474 Planarity : 0.003 0.034 4272 Dihedral : 7.293 57.501 3714 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.58 % Allowed : 5.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.16), residues: 2942 helix: 1.63 (0.21), residues: 674 sheet: 0.90 (0.17), residues: 832 loop : 0.66 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 91 HIS 0.003 0.001 HIS J 132 PHE 0.009 0.001 PHE B 342 TYR 0.013 0.001 TYR J 95 ARG 0.007 0.000 ARG J 100 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01233 ( 16) link_ALPHA2-6 : angle 3.30255 ( 48) hydrogen bonds : bond 0.03497 ( 1096) hydrogen bonds : angle 4.25712 ( 3042) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.51119 ( 4) glycosidic custom : bond 0.00487 ( 2) glycosidic custom : angle 4.00017 ( 6) covalent geometry : bond 0.00269 (24188) covalent geometry : angle 0.47794 (32810) *********************** 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 163 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 2.696 Fit side-chains REVERT: B 18 GLN cc_start: 0.8852 (mt0) cc_final: 0.8567 (mt0) REVERT: B 288 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.9049 (mmt) REVERT: A 502 ARG cc_start: 0.7910 (ttm110) cc_final: 0.7701 (mtp-110) REVERT: A 561 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7528 (tmt) REVERT: A 709 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8123 (mm-30) REVERT: A 988 LYS cc_start: 0.8735 (mppt) cc_final: 0.8327 (mppt) REVERT: J 18 GLN cc_start: 0.8848 (mt0) cc_final: 0.8528 (mt0) REVERT: J 288 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.9055 (mmt) REVERT: I 561 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7600 (tmt) REVERT: I 709 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8119 (mm-30) REVERT: I 988 LYS cc_start: 0.8736 (mppt) cc_final: 0.8322 (mppt) outliers start: 39 outliers final: 11 residues processed: 144 average time/residue: 1.5339 time to fit residues: 252.1384 Evaluate side-chains 124 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain A residue 306 GLN 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 J residue 288 MET Chi-restraints excluded: chain I residue 306 GLN 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 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 236 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN A 153 ASN A 702 GLN J 179 GLN I 153 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.080272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.066177 restraints weight = 41596.014| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.87 r_work: 0.2815 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24208 Z= 0.134 Angle : 0.473 11.270 32868 Z= 0.249 Chirality : 0.042 0.156 3474 Planarity : 0.003 0.032 4272 Dihedral : 5.793 46.505 3714 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.46 % Allowed : 6.75 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.16), residues: 2942 helix: 1.58 (0.21), residues: 674 sheet: 0.99 (0.17), residues: 808 loop : 0.54 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 91 HIS 0.003 0.001 HIS J 132 PHE 0.009 0.001 PHE B 342 TYR 0.013 0.001 TYR A 422 ARG 0.009 0.000 ARG I 502 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01325 ( 16) link_ALPHA2-6 : angle 2.61852 ( 48) hydrogen bonds : bond 0.03702 ( 1096) hydrogen bonds : angle 4.29329 ( 3042) SS BOND : bond 0.00255 ( 2) SS BOND : angle 0.74525 ( 4) glycosidic custom : bond 0.01193 ( 2) glycosidic custom : angle 2.34682 ( 6) covalent geometry : bond 0.00295 (24188) covalent geometry : angle 0.46188 (32810) *********************** 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 153 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 2.778 Fit side-chains REVERT: B 18 GLN cc_start: 0.8854 (mt0) cc_final: 0.8513 (mt0) REVERT: B 203 TYR cc_start: 0.9376 (OUTLIER) cc_final: 0.8667 (t80) REVERT: A 427 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8038 (mtt) REVERT: A 502 ARG cc_start: 0.8035 (ttm110) cc_final: 0.7762 (mtp-110) REVERT: A 561 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7612 (tmt) REVERT: A 988 LYS cc_start: 0.8709 (mppt) cc_final: 0.8307 (mppt) REVERT: J 18 GLN cc_start: 0.8844 (mt0) cc_final: 0.8495 (mt0) REVERT: J 203 TYR cc_start: 0.9373 (OUTLIER) cc_final: 0.8665 (t80) REVERT: I 213 LYS cc_start: 0.8522 (mtmt) cc_final: 0.8311 (mmpt) REVERT: I 502 ARG cc_start: 0.8195 (mtp-110) cc_final: 0.7835 (mtp-110) REVERT: I 561 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7628 (tmt) REVERT: I 988 LYS cc_start: 0.8740 (mppt) cc_final: 0.8330 (mppt) outliers start: 36 outliers final: 13 residues processed: 139 average time/residue: 1.5273 time to fit residues: 243.1694 Evaluate side-chains 128 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 2.653 ------------------------------------------------------------------------------- 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 427 MET 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 J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 306 GLN Chi-restraints excluded: chain I residue 352 LEU 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 767 ASN Chi-restraints excluded: chain I residue 769 SER Chi-restraints excluded: chain I residue 909 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 110 optimal weight: 4.9990 chunk 199 optimal weight: 0.0470 chunk 235 optimal weight: 2.9990 chunk 174 optimal weight: 0.3980 chunk 95 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 178 optimal weight: 0.6980 chunk 243 optimal weight: 6.9990 chunk 234 optimal weight: 0.6980 chunk 282 optimal weight: 4.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 702 GLN A 767 ASN I 362 HIS I 489 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.079834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.065685 restraints weight = 42197.589| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.88 r_work: 0.2817 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24208 Z= 0.121 Angle : 0.460 9.109 32868 Z= 0.242 Chirality : 0.042 0.159 3474 Planarity : 0.003 0.032 4272 Dihedral : 5.226 48.345 3714 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.46 % Allowed : 7.60 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.16), residues: 2942 helix: 1.49 (0.20), residues: 686 sheet: 0.95 (0.17), residues: 826 loop : 0.50 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 91 HIS 0.003 0.001 HIS B 132 PHE 0.009 0.001 PHE J 342 TYR 0.011 0.001 TYR B 95 ARG 0.004 0.000 ARG I 502 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01200 ( 16) link_ALPHA2-6 : angle 2.68252 ( 48) hydrogen bonds : bond 0.03432 ( 1096) hydrogen bonds : angle 4.26899 ( 3042) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.52366 ( 4) glycosidic custom : bond 0.00847 ( 2) glycosidic custom : angle 2.84889 ( 6) covalent geometry : bond 0.00268 (24188) covalent geometry : angle 0.44736 (32810) *********************** 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 151 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 2.791 Fit side-chains REVERT: B 18 GLN cc_start: 0.8847 (mt0) cc_final: 0.8537 (mt0) REVERT: B 203 TYR cc_start: 0.9360 (OUTLIER) cc_final: 0.8603 (t80) REVERT: A 502 ARG cc_start: 0.8159 (ttm110) cc_final: 0.7849 (mtp-110) REVERT: A 561 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7610 (tmt) REVERT: A 709 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8198 (mm-30) REVERT: A 988 LYS cc_start: 0.8725 (mppt) cc_final: 0.8328 (mppt) REVERT: J 18 GLN cc_start: 0.8840 (mt0) cc_final: 0.8527 (mt0) REVERT: J 203 TYR cc_start: 0.9357 (OUTLIER) cc_final: 0.8594 (t80) REVERT: I 502 ARG cc_start: 0.8215 (mtp-110) cc_final: 0.7906 (mtm-85) REVERT: I 561 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7736 (tmt) REVERT: I 709 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8148 (mm-30) REVERT: I 988 LYS cc_start: 0.8731 (mppt) cc_final: 0.8348 (mppt) outliers start: 36 outliers final: 16 residues processed: 139 average time/residue: 1.4908 time to fit residues: 238.1806 Evaluate side-chains 131 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 2.543 ------------------------------------------------------------------------------- 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 306 GLN 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 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 306 GLN 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 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 9 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 226 optimal weight: 0.4980 chunk 166 optimal weight: 4.9990 chunk 229 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 ASN A 489 ASN A 767 ASN J 283 ASN I 489 ASN 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 = 0.3140 r_free = 0.3140 target = 0.076898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.062524 restraints weight = 41748.315| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.88 r_work: 0.2745 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24208 Z= 0.185 Angle : 0.503 10.673 32868 Z= 0.266 Chirality : 0.043 0.157 3474 Planarity : 0.003 0.052 4272 Dihedral : 5.349 50.051 3714 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.66 % Allowed : 8.12 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.15), residues: 2942 helix: 1.36 (0.20), residues: 680 sheet: 0.91 (0.17), residues: 826 loop : 0.31 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 486 HIS 0.004 0.001 HIS B 132 PHE 0.010 0.001 PHE J 71 TYR 0.015 0.001 TYR I 422 ARG 0.008 0.000 ARG B 100 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01184 ( 16) link_ALPHA2-6 : angle 2.73153 ( 48) hydrogen bonds : bond 0.04017 ( 1096) hydrogen bonds : angle 4.48788 ( 3042) SS BOND : bond 0.00348 ( 2) SS BOND : angle 0.36659 ( 4) glycosidic custom : bond 0.01242 ( 2) glycosidic custom : angle 2.62587 ( 6) covalent geometry : bond 0.00423 (24188) covalent geometry : angle 0.49102 (32810) *********************** 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 154 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 2.799 Fit side-chains REVERT: B 18 GLN cc_start: 0.8852 (mt0) cc_final: 0.8487 (mt0) REVERT: B 203 TYR cc_start: 0.9406 (OUTLIER) cc_final: 0.8639 (t80) REVERT: A 561 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7699 (tmt) REVERT: A 709 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8139 (mm-30) REVERT: A 988 LYS cc_start: 0.8766 (mppt) cc_final: 0.8376 (mppt) REVERT: J 18 GLN cc_start: 0.8831 (mt0) cc_final: 0.8449 (mt0) REVERT: J 203 TYR cc_start: 0.9402 (OUTLIER) cc_final: 0.8632 (t80) REVERT: I 502 ARG cc_start: 0.8265 (mtp-110) cc_final: 0.7907 (mtm-85) REVERT: I 561 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7783 (tmt) REVERT: I 709 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8114 (mm-30) REVERT: I 988 LYS cc_start: 0.8771 (mppt) cc_final: 0.8375 (mppt) outliers start: 41 outliers final: 16 residues processed: 139 average time/residue: 1.3984 time to fit residues: 224.4479 Evaluate side-chains 135 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 2.596 ------------------------------------------------------------------------------- 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 356 ILE 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 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 356 ILE 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 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 179 optimal weight: 6.9990 chunk 230 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 258 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN 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 = 0.3151 r_free = 0.3151 target = 0.077384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.063140 restraints weight = 41547.063| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.87 r_work: 0.2752 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24208 Z= 0.152 Angle : 0.483 11.516 32868 Z= 0.256 Chirality : 0.042 0.151 3474 Planarity : 0.003 0.034 4272 Dihedral : 5.225 50.683 3714 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.41 % Allowed : 8.77 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.15), residues: 2942 helix: 1.31 (0.20), residues: 680 sheet: 0.88 (0.17), residues: 826 loop : 0.29 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 91 HIS 0.003 0.001 HIS A 362 PHE 0.009 0.001 PHE B 342 TYR 0.012 0.001 TYR A 422 ARG 0.007 0.000 ARG J 100 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01187 ( 16) link_ALPHA2-6 : angle 2.71131 ( 48) hydrogen bonds : bond 0.03747 ( 1096) hydrogen bonds : angle 4.46314 ( 3042) SS BOND : bond 0.00332 ( 2) SS BOND : angle 1.31253 ( 4) glycosidic custom : bond 0.01001 ( 2) glycosidic custom : angle 2.72314 ( 6) covalent geometry : bond 0.00344 (24188) covalent geometry : angle 0.47102 (32810) *********************** 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 151 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 2.593 Fit side-chains REVERT: B 18 GLN cc_start: 0.8822 (mt0) cc_final: 0.8445 (mt0) REVERT: B 203 TYR cc_start: 0.9376 (OUTLIER) cc_final: 0.8600 (t80) REVERT: A 561 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7746 (tmt) REVERT: A 709 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8154 (mm-30) REVERT: A 988 LYS cc_start: 0.8764 (mppt) cc_final: 0.8334 (mppt) REVERT: J 18 GLN cc_start: 0.8808 (mt0) cc_final: 0.8424 (mt0) REVERT: J 203 TYR cc_start: 0.9370 (OUTLIER) cc_final: 0.8587 (t80) REVERT: I 502 ARG cc_start: 0.8274 (mtp-110) cc_final: 0.7908 (mtm-85) REVERT: I 561 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7792 (tmt) REVERT: I 709 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8127 (mm-30) REVERT: I 763 ASP cc_start: 0.7954 (t70) cc_final: 0.7753 (t0) REVERT: I 988 LYS cc_start: 0.8775 (mppt) cc_final: 0.8345 (mppt) outliers start: 35 outliers final: 13 residues processed: 135 average time/residue: 1.4436 time to fit residues: 224.7999 Evaluate side-chains 135 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 2.572 ------------------------------------------------------------------------------- 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 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 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 306 GLN 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 909 THR Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 181 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 282 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 228 optimal weight: 6.9990 chunk 225 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN A 767 ASN I 489 ASN I 677 GLN I 767 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.073217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.058046 restraints weight = 40982.768| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 1.92 r_work: 0.2576 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 24208 Z= 0.310 Angle : 0.591 14.680 32868 Z= 0.311 Chirality : 0.047 0.154 3474 Planarity : 0.004 0.068 4272 Dihedral : 5.832 53.460 3714 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.54 % Allowed : 8.89 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 2942 helix: 1.00 (0.20), residues: 676 sheet: 0.95 (0.18), residues: 806 loop : 0.10 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 36 HIS 0.006 0.001 HIS A 362 PHE 0.012 0.002 PHE J 71 TYR 0.018 0.002 TYR I 422 ARG 0.007 0.001 ARG B 100 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01091 ( 16) link_ALPHA2-6 : angle 2.86852 ( 48) hydrogen bonds : bond 0.04798 ( 1096) hydrogen bonds : angle 4.84989 ( 3042) SS BOND : bond 0.00419 ( 2) SS BOND : angle 1.66474 ( 4) glycosidic custom : bond 0.01260 ( 2) glycosidic custom : angle 2.62966 ( 6) covalent geometry : bond 0.00722 (24188) covalent geometry : angle 0.58011 (32810) *********************** 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 153 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 2.573 Fit side-chains REVERT: B 18 GLN cc_start: 0.8797 (mt0) cc_final: 0.8134 (mt0) REVERT: B 203 TYR cc_start: 0.9481 (OUTLIER) cc_final: 0.8650 (t80) REVERT: A 561 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7791 (tmt) REVERT: A 988 LYS cc_start: 0.8805 (mppt) cc_final: 0.8354 (mppt) REVERT: J 18 GLN cc_start: 0.8804 (mt0) cc_final: 0.8155 (mt0) REVERT: J 203 TYR cc_start: 0.9471 (OUTLIER) cc_final: 0.8765 (t80) REVERT: I 502 ARG cc_start: 0.8330 (mtp-110) cc_final: 0.7982 (mtm-85) REVERT: I 561 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7839 (tmt) REVERT: I 988 LYS cc_start: 0.8778 (mppt) cc_final: 0.8335 (mppt) outliers start: 38 outliers final: 14 residues processed: 138 average time/residue: 1.6017 time to fit residues: 251.5274 Evaluate side-chains 128 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 2.658 ------------------------------------------------------------------------------- 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 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 909 THR Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 76 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 11 optimal weight: 0.0060 chunk 57 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN A 434 ASN A 767 ASN I 434 ASN I 767 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.078014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.063916 restraints weight = 41170.173| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.84 r_work: 0.2760 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24208 Z= 0.116 Angle : 0.479 13.832 32868 Z= 0.255 Chirality : 0.042 0.145 3474 Planarity : 0.003 0.031 4272 Dihedral : 5.239 52.673 3714 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.17 % Allowed : 9.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 2942 helix: 1.19 (0.20), residues: 680 sheet: 0.97 (0.18), residues: 802 loop : 0.15 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 91 HIS 0.003 0.001 HIS J 132 PHE 0.011 0.001 PHE I 606 TYR 0.010 0.001 TYR B 95 ARG 0.002 0.000 ARG I 502 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01155 ( 16) link_ALPHA2-6 : angle 2.66685 ( 48) hydrogen bonds : bond 0.03573 ( 1096) hydrogen bonds : angle 4.54918 ( 3042) SS BOND : bond 0.00392 ( 2) SS BOND : angle 1.04451 ( 4) glycosidic custom : bond 0.00930 ( 2) glycosidic custom : angle 2.78743 ( 6) covalent geometry : bond 0.00254 (24188) covalent geometry : angle 0.46684 (32810) *********************** 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 148 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 2.956 Fit side-chains REVERT: B 18 GLN cc_start: 0.8776 (mt0) cc_final: 0.8416 (mt0) REVERT: B 203 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.8716 (t80) REVERT: A 506 MET cc_start: 0.8836 (ttt) cc_final: 0.8592 (ppp) REVERT: A 561 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7766 (tmt) REVERT: A 709 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8165 (mm-30) REVERT: A 988 LYS cc_start: 0.8799 (mppt) cc_final: 0.8378 (mppt) REVERT: J 18 GLN cc_start: 0.8788 (mt0) cc_final: 0.8433 (mt0) REVERT: J 203 TYR cc_start: 0.9349 (OUTLIER) cc_final: 0.8700 (t80) REVERT: I 502 ARG cc_start: 0.8312 (mtp-110) cc_final: 0.7976 (mtm-85) REVERT: I 506 MET cc_start: 0.8848 (ttt) cc_final: 0.8616 (ppp) REVERT: I 561 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7845 (tmt) REVERT: I 709 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8176 (mm-30) REVERT: I 988 LYS cc_start: 0.8801 (mppt) cc_final: 0.8375 (mppt) outliers start: 29 outliers final: 10 residues processed: 138 average time/residue: 1.5286 time to fit residues: 243.5378 Evaluate side-chains 131 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 2.989 ------------------------------------------------------------------------------- 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 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 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 769 SER Chi-restraints excluded: chain I residue 893 LYS Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 166 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 287 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 202 optimal weight: 0.0470 overall best weight: 1.5082 ------------------------------------------------------------------------------- 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 702 GLN I 749 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.075330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.060177 restraints weight = 40507.982| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.93 r_work: 0.2624 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2538 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= 0.167 Angle : 0.507 12.046 32868 Z= 0.268 Chirality : 0.043 0.186 3474 Planarity : 0.003 0.043 4272 Dihedral : 5.268 52.154 3714 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.93 % Allowed : 9.86 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 2942 helix: 1.18 (0.20), residues: 680 sheet: 0.93 (0.18), residues: 806 loop : 0.15 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 91 HIS 0.003 0.001 HIS J 132 PHE 0.009 0.001 PHE B 342 TYR 0.012 0.001 TYR I 422 ARG 0.004 0.000 ARG J 100 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01167 ( 16) link_ALPHA2-6 : angle 2.73892 ( 48) hydrogen bonds : bond 0.03865 ( 1096) hydrogen bonds : angle 4.57290 ( 3042) SS BOND : bond 0.00489 ( 2) SS BOND : angle 1.27080 ( 4) glycosidic custom : bond 0.01048 ( 2) glycosidic custom : angle 2.69179 ( 6) covalent geometry : bond 0.00381 (24188) covalent geometry : angle 0.49537 (32810) *********************** 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 139 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 2.683 Fit side-chains REVERT: B 7 ARG cc_start: 0.7900 (ttp-170) cc_final: 0.7523 (ttm170) REVERT: B 18 GLN cc_start: 0.8802 (mt0) cc_final: 0.8422 (mt0) REVERT: B 203 TYR cc_start: 0.9401 (OUTLIER) cc_final: 0.8633 (t80) REVERT: A 561 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7765 (tmt) REVERT: A 709 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8187 (mm-30) REVERT: A 893 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.8652 (ptpt) REVERT: A 988 LYS cc_start: 0.8827 (mppt) cc_final: 0.8410 (mppt) REVERT: J 18 GLN cc_start: 0.8820 (mt0) cc_final: 0.8447 (mt0) REVERT: J 203 TYR cc_start: 0.9394 (OUTLIER) cc_final: 0.8617 (t80) REVERT: I 502 ARG cc_start: 0.8322 (mtp-110) cc_final: 0.7971 (mtm-85) REVERT: I 561 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7772 (tmt) REVERT: I 709 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8196 (mm-30) REVERT: I 893 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.8678 (ptpt) REVERT: I 988 LYS cc_start: 0.8793 (mppt) cc_final: 0.8345 (mppt) outliers start: 23 outliers final: 9 residues processed: 133 average time/residue: 1.5953 time to fit residues: 241.9159 Evaluate side-chains 131 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 2.609 ------------------------------------------------------------------------------- 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 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 893 LYS 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 769 SER Chi-restraints excluded: chain I residue 893 LYS Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 246 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 69 optimal weight: 0.1980 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 489 ASN A 749 ASN I 702 GLN I 749 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.077704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.063585 restraints weight = 41601.474| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.87 r_work: 0.2761 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24208 Z= 0.115 Angle : 0.478 11.394 32868 Z= 0.253 Chirality : 0.042 0.154 3474 Planarity : 0.003 0.031 4272 Dihedral : 5.033 52.194 3714 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.73 % Allowed : 10.06 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.15), residues: 2942 helix: 1.24 (0.20), residues: 680 sheet: 0.98 (0.18), residues: 802 loop : 0.19 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 91 HIS 0.003 0.001 HIS A 362 PHE 0.009 0.001 PHE A 438 TYR 0.011 0.001 TYR A 565 ARG 0.003 0.000 ARG B 100 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01214 ( 16) link_ALPHA2-6 : angle 2.67729 ( 48) hydrogen bonds : bond 0.03447 ( 1096) hydrogen bonds : angle 4.44218 ( 3042) SS BOND : bond 0.00392 ( 2) SS BOND : angle 1.06597 ( 4) glycosidic custom : bond 0.01022 ( 2) glycosidic custom : angle 2.72985 ( 6) covalent geometry : bond 0.00253 (24188) covalent geometry : angle 0.46606 (32810) ********************** 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 134 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 2.579 Fit side-chains REVERT: B 7 ARG cc_start: 0.7926 (ttp-170) cc_final: 0.7553 (ttm170) REVERT: B 18 GLN cc_start: 0.8780 (mt0) cc_final: 0.8454 (mt0) REVERT: B 203 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.8699 (t80) REVERT: A 506 MET cc_start: 0.8838 (ttt) cc_final: 0.8591 (ppp) REVERT: A 561 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7718 (tmt) REVERT: A 709 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8179 (mm-30) REVERT: A 988 LYS cc_start: 0.8851 (mppt) cc_final: 0.8520 (mppt) REVERT: J 18 GLN cc_start: 0.8782 (mt0) cc_final: 0.8428 (mt0) REVERT: J 203 TYR cc_start: 0.9341 (OUTLIER) cc_final: 0.8674 (t80) REVERT: I 502 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.7951 (mtm-85) REVERT: I 506 MET cc_start: 0.8837 (ttt) cc_final: 0.8593 (ppp) REVERT: I 561 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7784 (tmt) REVERT: I 709 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8185 (mm-30) REVERT: I 893 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.8687 (ptpt) REVERT: I 988 LYS cc_start: 0.8858 (mppt) cc_final: 0.8450 (mppt) outliers start: 18 outliers final: 9 residues processed: 129 average time/residue: 1.5174 time to fit residues: 223.4131 Evaluate side-chains 130 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 2.562 ------------------------------------------------------------------------------- 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 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 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 769 SER Chi-restraints excluded: chain I residue 893 LYS Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 233 optimal weight: 0.2980 chunk 190 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 293 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 749 ASN I 489 ASN I 749 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.075089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.060003 restraints weight = 40686.164| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 1.92 r_work: 0.2621 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2558 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= 0.174 Angle : 0.506 10.616 32868 Z= 0.268 Chirality : 0.043 0.146 3474 Planarity : 0.003 0.044 4272 Dihedral : 5.184 52.987 3714 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.89 % Allowed : 9.90 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 2942 helix: 1.20 (0.20), residues: 680 sheet: 0.91 (0.18), residues: 806 loop : 0.15 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 91 HIS 0.003 0.001 HIS I 362 PHE 0.009 0.001 PHE J 342 TYR 0.013 0.001 TYR B 95 ARG 0.004 0.000 ARG J 100 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01162 ( 16) link_ALPHA2-6 : angle 2.74752 ( 48) hydrogen bonds : bond 0.03890 ( 1096) hydrogen bonds : angle 4.54521 ( 3042) SS BOND : bond 0.00449 ( 2) SS BOND : angle 1.19056 ( 4) glycosidic custom : bond 0.01070 ( 2) glycosidic custom : angle 2.64677 ( 6) covalent geometry : bond 0.00398 (24188) covalent geometry : angle 0.49426 (32810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13070.15 seconds wall clock time: 226 minutes 47.67 seconds (13607.67 seconds total)