Starting phenix.real_space_refine on Fri Feb 6 06:33:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aa1_15290/02_2026/8aa1_15290.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aa1_15290/02_2026/8aa1_15290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8aa1_15290/02_2026/8aa1_15290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aa1_15290/02_2026/8aa1_15290.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8aa1_15290/02_2026/8aa1_15290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aa1_15290/02_2026/8aa1_15290.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.39, per 1000 atoms: 0.19 Number of scatterers: 23634 At special positions: 0 Unit cell: (148.035, 96.915, 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=2.04 Simple disulfide: pdb=" SG CYS J 387 " - pdb=" SG CYS J 389 " distance=2.04 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 3 " - " FRU C 7 " ~> Even though FRU is a beta isomer, an alpha linkage is required... " FRU K 3 " - " 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: 1.78 Conformation dependent library (CDL) restraints added in 752.5 milliseconds 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: 82 helices and 28 sheets defined 27.9% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'B' and resid 24 through 39 removed outlier: 4.427A pdb=" N TRP B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.894A pdb=" N VAL B 53 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 3.976A 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: 3.531A pdb=" N ASN B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 3.849A 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 153 through 160 removed outlier: 3.583A pdb=" N ASN B 158 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 185 removed outlier: 3.968A pdb=" N ASP B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 213 removed outlier: 3.779A pdb=" N TYR B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 removed outlier: 3.525A pdb=" N LEU B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 245 removed outlier: 3.537A pdb=" N MET B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY B 245 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.840A pdb=" N LEU B 258 " --> pdb=" O MET B 255 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.563A pdb=" N GLU B 262 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 292 removed outlier: 4.614A pdb=" N LEU B 290 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 3.611A 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: 3.528A pdb=" N VAL B 309 " --> pdb=" O SER B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 342 Processing helix chain 'B' and resid 407 through 422 Processing helix chain 'B' and resid 425 through 442 removed outlier: 3.742A pdb=" N ALA B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 453 removed outlier: 3.738A pdb=" N LYS B 451 " --> pdb=" O PHE B 448 " (cutoff:3.500A) 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 513 Processing helix chain 'B' and resid 516 through 521 removed outlier: 4.418A pdb=" N ASN B 521 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 542 Processing helix chain 'A' and resid 105 through 112 removed outlier: 3.642A pdb=" N LYS A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 4.006A 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: 3.986A pdb=" N GLU A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.549A pdb=" N ASN A 255 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 4.488A 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 601 through 608 removed outlier: 5.604A pdb=" N ASN A 605 " --> pdb=" O THR A 602 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE A 606 " --> pdb=" O GLN A 603 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET A 607 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS A 608 " --> pdb=" O ASN A 605 " (cutoff:3.500A) 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: 4.073A pdb=" N LYS A 892 " --> pdb=" O SER A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 914 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: 4.427A pdb=" N TRP J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA J 37 " --> pdb=" O TYR J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 55 removed outlier: 3.895A pdb=" N VAL J 53 " --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 3.977A 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: 3.532A pdb=" N ASN J 88 " --> pdb=" O ASP J 84 " (cutoff:3.500A) removed outlier: 3.848A 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 153 through 160 removed outlier: 3.583A pdb=" N ASN J 158 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 185 removed outlier: 3.968A pdb=" N ASP J 177 " --> pdb=" O LYS J 173 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE J 178 " --> pdb=" O ILE J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 213 removed outlier: 3.778A pdb=" N TYR J 213 " --> pdb=" O LEU J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 237 removed outlier: 3.525A pdb=" N LEU J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 245 removed outlier: 3.537A pdb=" N MET J 242 " --> pdb=" O ASP J 238 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY J 245 " --> pdb=" O ILE J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 262 removed outlier: 3.840A pdb=" N LEU J 258 " --> pdb=" O MET J 255 " (cutoff:3.500A) Proline residue: J 259 - end of helix removed outlier: 3.563A pdb=" N GLU J 262 " --> pdb=" O PRO J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 292 removed outlier: 4.614A pdb=" N LEU J 290 " --> pdb=" O GLY J 287 " (cutoff:3.500A) removed outlier: 3.612A 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: 3.528A pdb=" N VAL J 309 " --> pdb=" O SER J 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 342 Processing helix chain 'J' and resid 407 through 422 Processing helix chain 'J' and resid 425 through 442 removed outlier: 3.743A pdb=" N ALA J 429 " --> pdb=" O ARG J 425 " (cutoff:3.500A) Processing helix chain 'J' and resid 447 through 453 removed outlier: 3.737A pdb=" N LYS J 451 " --> pdb=" O PHE J 448 " (cutoff:3.500A) 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 513 Processing helix chain 'J' and resid 516 through 521 removed outlier: 4.418A pdb=" N ASN J 521 " --> pdb=" O ILE J 518 " (cutoff:3.500A) Processing helix chain 'J' and resid 535 through 542 Processing helix chain 'I' and resid 105 through 112 removed outlier: 3.642A pdb=" N LYS I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 4.005A 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: 3.986A pdb=" N GLU I 170 " --> pdb=" O GLY I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 Processing helix chain 'I' and resid 190 through 192 No H-bonds generated for 'chain 'I' and resid 190 through 192' Processing helix chain 'I' and resid 233 through 249 Processing helix chain 'I' and resid 251 through 256 removed outlier: 3.549A pdb=" N ASN I 255 " --> pdb=" O PRO I 252 " (cutoff:3.500A) removed outlier: 4.488A 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 601 through 608 removed outlier: 5.604A pdb=" N ASN I 605 " --> pdb=" O THR I 602 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE I 606 " --> pdb=" O GLN I 603 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET I 607 " --> pdb=" O GLU I 604 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS I 608 " --> pdb=" O ASN I 605 " (cutoff:3.500A) 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: 4.072A pdb=" N LYS I 892 " --> pdb=" O SER I 888 " (cutoff:3.500A) Processing helix chain 'I' and resid 908 through 914 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: 7.230A pdb=" N SER B 267 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG B 406 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TRP B 269 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 3.969A 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: 4.071A pdb=" N ILE A 179 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 178 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 156 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE A 202 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE A 158 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.234A 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: 3.881A pdb=" N VAL A 304 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG A 421 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG A 457 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N THR A 591 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLY A 626 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA A 740 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN A 879 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU A 951 " --> pdb=" O GLN A 879 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL A 881 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 5.368A 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: 6.611A pdb=" N ALA A 260 " --> pdb=" O MET A 276 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N MET A 276 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 6.747A 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: 6.411A 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: 6.459A 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: 4.859A 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: 7.230A pdb=" N SER J 267 " --> pdb=" O ARG J 406 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG J 406 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TRP J 269 " --> pdb=" O VAL J 404 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 313 through 314 removed outlier: 3.969A 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: 4.071A pdb=" N ILE I 179 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER I 178 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU I 156 " --> pdb=" O ILE I 200 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE I 202 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE I 158 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 7.235A 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: 3.880A pdb=" N VAL I 304 " --> pdb=" O LEU I 331 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG I 421 " --> pdb=" O ARG I 457 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG I 457 " --> pdb=" O ARG I 421 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N THR I 591 " --> pdb=" O GLY I 626 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLY I 626 " --> pdb=" O THR I 591 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA I 740 " --> pdb=" O LEU I 776 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN I 879 " --> pdb=" O LEU I 951 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU I 951 " --> pdb=" O GLN I 879 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL I 881 " --> pdb=" O LEU I 949 " (cutoff:3.500A) removed outlier: 5.367A 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: 6.611A pdb=" N ALA I 260 " --> pdb=" O MET I 276 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET I 276 " --> pdb=" O ALA I 260 " (cutoff:3.500A) removed outlier: 6.746A 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: 6.411A 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: 6.459A 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: 4.858A 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 1104 hydrogen bonds defined for protein. 3012 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.61 Time building geometry restraints manager: 2.31 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: 6037 1.46 - 1.58: 10163 1.58 - 1.70: 66 1.70 - 1.81: 148 Bond restraints: 24188 Sorted by residual: bond pdb=" C2 FRU C 7 " pdb=" O5 FRU C 7 " ideal model delta sigma weight residual 1.412 1.643 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C2 FRU L 4 " pdb=" O5 FRU L 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 3 " pdb=" O5 FRU K 3 " 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 L 3 " pdb=" O5 FRU L 3 " ideal model delta sigma weight residual 1.412 1.641 -0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2 FRU D 4 " pdb=" O5 FRU D 4 " ideal model delta sigma weight residual 1.412 1.641 -0.229 2.00e-02 2.50e+03 1.32e+02 ... (remaining 24183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 32369 2.00 - 3.99: 323 3.99 - 5.99: 102 5.99 - 7.98: 12 7.98 - 9.98: 4 Bond angle restraints: 32810 Sorted by residual: angle pdb=" C CYS B 298 " pdb=" N CYS B 299 " pdb=" CA CYS B 299 " ideal model delta sigma weight residual 121.54 129.62 -8.08 1.91e+00 2.74e-01 1.79e+01 angle pdb=" C CYS J 298 " pdb=" N CYS J 299 " pdb=" CA CYS J 299 " ideal model delta sigma weight residual 121.54 129.58 -8.04 1.91e+00 2.74e-01 1.77e+01 angle pdb=" CA LYS A 318 " pdb=" CB LYS A 318 " pdb=" CG LYS A 318 " ideal model delta sigma weight residual 114.10 120.88 -6.78 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA LYS I 318 " pdb=" CB LYS I 318 " pdb=" CG LYS I 318 " ideal model delta sigma weight residual 114.10 120.88 -6.78 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CB MET I 427 " pdb=" CG MET I 427 " pdb=" SD MET I 427 " ideal model delta sigma weight residual 112.70 102.72 9.98 3.00e+00 1.11e-01 1.11e+01 ... (remaining 32805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 13441 17.05 - 34.10: 727 34.10 - 51.15: 232 51.15 - 68.20: 74 68.20 - 85.25: 8 Dihedral angle restraints: 14482 sinusoidal: 5990 harmonic: 8492 Sorted by residual: dihedral pdb=" CA ARG J 7 " pdb=" C ARG J 7 " pdb=" N GLN J 8 " pdb=" CA GLN J 8 " ideal model delta harmonic sigma weight residual 180.00 -160.73 -19.27 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ARG B 7 " pdb=" C ARG B 7 " pdb=" N GLN B 8 " pdb=" CA GLN B 8 " ideal model delta harmonic sigma weight residual -180.00 -160.73 -19.27 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA CYS B 387 " pdb=" C CYS B 387 " pdb=" N ASP B 388 " pdb=" CA ASP B 388 " ideal model delta harmonic sigma weight residual 180.00 -161.83 -18.17 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 14479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2380 0.038 - 0.077: 793 0.077 - 0.115: 244 0.115 - 0.153: 53 0.153 - 0.192: 4 Chirality restraints: 3474 Sorted by residual: chirality pdb=" C2 FRU K 7 " pdb=" O1 FRU K 3 " pdb=" C1 FRU K 7 " pdb=" O5 FRU K 7 " both_signs ideal model delta sigma weight residual False 2.60 2.79 -0.19 2.00e-02 2.50e+03 9.19e+01 chirality pdb=" C2 FRU C 7 " pdb=" O1 FRU C 3 " pdb=" C1 FRU C 7 " pdb=" O5 FRU C 7 " both_signs ideal model delta sigma weight residual False 2.60 2.79 -0.19 2.00e-02 2.50e+03 9.04e+01 chirality pdb=" C2 FRU L 4 " pdb=" O6 FRU L 3 " pdb=" C1 FRU L 4 " pdb=" O5 FRU L 4 " both_signs ideal model delta sigma weight residual False 2.60 2.68 -0.08 2.00e-02 2.50e+03 1.41e+01 ... (remaining 3471 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 592 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO A 593 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 593 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 593 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE I 592 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.89e+00 pdb=" N PRO I 593 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO I 593 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 593 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 530 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO I 531 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO I 531 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 531 " 0.016 5.00e-02 4.00e+02 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 335 2.63 - 3.20: 20526 3.20 - 3.76: 37434 3.76 - 4.33: 54951 4.33 - 4.90: 90820 Nonbonded interactions: 204066 Sorted by model distance: nonbonded pdb=" OD1 ASN J 401 " pdb="MG MG J 601 " model vdw 2.061 2.170 nonbonded pdb=" OD1 ASN B 401 " pdb="MG MG B 601 " model vdw 2.062 2.170 nonbonded pdb=" OD1 ASN A 841 " pdb="MG MG A1101 " model vdw 2.107 2.170 nonbonded pdb=" OD1 ASN I 841 " pdb="MG MG I1101 " model vdw 2.107 2.170 nonbonded pdb=" OD2 ASP A 848 " pdb="MG MG A1101 " model vdw 2.108 2.170 ... (remaining 204061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.700 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 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 0.231 24208 Z= 0.539 Angle : 0.568 9.977 32868 Z= 0.271 Chirality : 0.043 0.192 3474 Planarity : 0.003 0.034 4272 Dihedral : 12.372 85.254 9116 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.56 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.16), residues: 2942 helix: 1.65 (0.21), residues: 670 sheet: 0.97 (0.18), residues: 794 loop : 0.39 (0.17), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 7 TYR 0.011 0.001 TYR I 225 PHE 0.010 0.001 PHE J 301 TRP 0.012 0.001 TRP J 91 HIS 0.002 0.000 HIS J 302 Details of bonding type rmsd covalent geometry : bond 0.01056 (24188) covalent geometry : angle 0.54916 (32810) SS BOND : bond 0.00497 ( 2) SS BOND : angle 0.51967 ( 4) hydrogen bonds : bond 0.12276 ( 1104) hydrogen bonds : angle 4.91105 ( 3012) glycosidic custom : bond 0.04027 ( 2) glycosidic custom : angle 3.73430 ( 6) link_ALPHA2-6 : bond 0.08356 ( 16) link_ALPHA2-6 : angle 3.60491 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.948 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 109 average time/residue: 0.6677 time to fit residues: 83.7043 Evaluate side-chains 101 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 1016 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 302 HIS A 955 GLN J 302 HIS I 955 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.078073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.063697 restraints weight = 43875.736| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.13 r_work: 0.2733 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24208 Z= 0.148 Angle : 0.526 8.836 32868 Z= 0.270 Chirality : 0.043 0.154 3474 Planarity : 0.003 0.031 4272 Dihedral : 7.249 59.275 3716 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.52 % Favored : 97.42 % Rotamer: Outliers : 0.57 % Allowed : 6.22 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.16), residues: 2942 helix: 1.59 (0.21), residues: 690 sheet: 0.81 (0.18), residues: 814 loop : 0.46 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 515 TYR 0.016 0.001 TYR J 33 PHE 0.013 0.001 PHE A 813 TRP 0.014 0.001 TRP A 878 HIS 0.003 0.001 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.00333 (24188) covalent geometry : angle 0.51061 (32810) SS BOND : bond 0.00308 ( 2) SS BOND : angle 0.67310 ( 4) hydrogen bonds : bond 0.03433 ( 1104) hydrogen bonds : angle 4.32029 ( 3012) glycosidic custom : bond 0.01171 ( 2) glycosidic custom : angle 2.17673 ( 6) link_ALPHA2-6 : bond 0.01103 ( 16) link_ALPHA2-6 : angle 3.20343 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.728 Fit side-chains REVERT: A 229 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8584 (mtt) REVERT: A 427 MET cc_start: 0.8615 (ttm) cc_final: 0.8295 (mtt) REVERT: I 229 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8573 (mtt) outliers start: 14 outliers final: 7 residues processed: 121 average time/residue: 0.7210 time to fit residues: 99.6425 Evaluate side-chains 109 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 516 CYS Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 1016 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 16 optimal weight: 6.9990 chunk 287 optimal weight: 5.9990 chunk 223 optimal weight: 0.9980 chunk 228 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 279 optimal weight: 0.0970 chunk 119 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 289 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 309 ASN I 151 ASN I 153 ASN I 309 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.078561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.064178 restraints weight = 44035.934| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.14 r_work: 0.2743 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24208 Z= 0.105 Angle : 0.469 8.152 32868 Z= 0.245 Chirality : 0.041 0.144 3474 Planarity : 0.003 0.035 4272 Dihedral : 5.839 55.340 3716 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.94 % Favored : 97.99 % Rotamer: Outliers : 0.85 % Allowed : 6.67 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.16), residues: 2942 helix: 1.63 (0.21), residues: 688 sheet: 0.79 (0.18), residues: 810 loop : 0.46 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 7 TYR 0.012 0.001 TYR A 225 PHE 0.008 0.001 PHE J 342 TRP 0.013 0.001 TRP A 878 HIS 0.003 0.001 HIS J 302 Details of bonding type rmsd covalent geometry : bond 0.00228 (24188) covalent geometry : angle 0.45791 (32810) SS BOND : bond 0.01306 ( 2) SS BOND : angle 0.91195 ( 4) hydrogen bonds : bond 0.03143 ( 1104) hydrogen bonds : angle 4.19936 ( 3012) glycosidic custom : bond 0.01575 ( 2) glycosidic custom : angle 1.88222 ( 6) link_ALPHA2-6 : bond 0.01330 ( 16) link_ALPHA2-6 : angle 2.58639 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.957 Fit side-chains REVERT: A 109 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8293 (mp) REVERT: A 427 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8157 (mtt) REVERT: A 767 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8412 (t0) REVERT: I 109 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8314 (mp) REVERT: I 767 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8407 (t0) outliers start: 21 outliers final: 5 residues processed: 121 average time/residue: 0.7387 time to fit residues: 102.1390 Evaluate side-chains 112 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 516 CYS Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 767 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 1 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 276 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 196 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.074571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.059970 restraints weight = 44056.062| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.12 r_work: 0.2646 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24208 Z= 0.209 Angle : 0.537 9.981 32868 Z= 0.283 Chirality : 0.044 0.155 3474 Planarity : 0.004 0.044 4272 Dihedral : 5.663 51.289 3714 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.09 % Favored : 96.84 % Rotamer: Outliers : 0.81 % Allowed : 7.03 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.16), residues: 2942 helix: 1.42 (0.21), residues: 686 sheet: 0.62 (0.17), residues: 836 loop : 0.38 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 513 TYR 0.015 0.001 TYR A 225 PHE 0.013 0.001 PHE B 342 TRP 0.010 0.001 TRP I 535 HIS 0.004 0.001 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.00480 (24188) covalent geometry : angle 0.52687 (32810) SS BOND : bond 0.00887 ( 2) SS BOND : angle 0.56014 ( 4) hydrogen bonds : bond 0.03876 ( 1104) hydrogen bonds : angle 4.42874 ( 3012) glycosidic custom : bond 0.01374 ( 2) glycosidic custom : angle 1.81087 ( 6) link_ALPHA2-6 : bond 0.01070 ( 16) link_ALPHA2-6 : angle 2.71507 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.889 Fit side-chains REVERT: A 229 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8498 (mtt) REVERT: A 427 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8469 (mtt) REVERT: I 229 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8509 (mtt) outliers start: 20 outliers final: 5 residues processed: 115 average time/residue: 0.7023 time to fit residues: 92.1020 Evaluate side-chains 109 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 1016 PHE Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 767 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 183 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 221 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 GLN J 43 ASN I 677 GLN I 744 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.073220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.058634 restraints weight = 44149.380| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.11 r_work: 0.2618 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 24208 Z= 0.258 Angle : 0.558 10.268 32868 Z= 0.295 Chirality : 0.045 0.181 3474 Planarity : 0.004 0.041 4272 Dihedral : 6.058 59.220 3714 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.97 % Rotamer: Outliers : 1.21 % Allowed : 7.56 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.15), residues: 2942 helix: 1.27 (0.20), residues: 690 sheet: 0.50 (0.17), residues: 826 loop : 0.18 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 7 TYR 0.018 0.002 TYR A 422 PHE 0.010 0.001 PHE I 813 TRP 0.012 0.001 TRP B 91 HIS 0.004 0.001 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.00596 (24188) covalent geometry : angle 0.54798 (32810) SS BOND : bond 0.00838 ( 2) SS BOND : angle 1.13303 ( 4) hydrogen bonds : bond 0.04095 ( 1104) hydrogen bonds : angle 4.58680 ( 3012) glycosidic custom : bond 0.01431 ( 2) glycosidic custom : angle 1.88248 ( 6) link_ALPHA2-6 : bond 0.00976 ( 16) link_ALPHA2-6 : angle 2.73391 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.684 Fit side-chains REVERT: B 7 ARG cc_start: 0.8259 (ptm160) cc_final: 0.8053 (ptm-80) REVERT: B 114 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8350 (mmpt) REVERT: A 229 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8437 (mtt) REVERT: A 427 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8456 (mtt) REVERT: J 7 ARG cc_start: 0.8244 (ptm160) cc_final: 0.8032 (ptm-80) REVERT: J 114 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8344 (mmpt) REVERT: I 229 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8434 (mtt) outliers start: 30 outliers final: 17 residues processed: 117 average time/residue: 0.7238 time to fit residues: 96.0686 Evaluate side-chains 118 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 1016 PHE Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 767 ASN Chi-restraints excluded: chain I residue 876 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.0070 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 259 optimal weight: 4.9990 chunk 198 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.075309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.060774 restraints weight = 43977.974| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.12 r_work: 0.2667 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24208 Z= 0.120 Angle : 0.484 9.091 32868 Z= 0.255 Chirality : 0.042 0.148 3474 Planarity : 0.003 0.037 4272 Dihedral : 5.681 59.731 3714 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.24 % Favored : 97.69 % Rotamer: Outliers : 0.93 % Allowed : 8.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2942 helix: 1.52 (0.21), residues: 668 sheet: 0.52 (0.17), residues: 834 loop : 0.28 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 7 TYR 0.012 0.001 TYR I 422 PHE 0.010 0.001 PHE B 301 TRP 0.014 0.001 TRP B 91 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00262 (24188) covalent geometry : angle 0.47336 (32810) SS BOND : bond 0.00765 ( 2) SS BOND : angle 0.83501 ( 4) hydrogen bonds : bond 0.03318 ( 1104) hydrogen bonds : angle 4.36171 ( 3012) glycosidic custom : bond 0.01403 ( 2) glycosidic custom : angle 1.96326 ( 6) link_ALPHA2-6 : bond 0.01207 ( 16) link_ALPHA2-6 : angle 2.58233 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.898 Fit side-chains REVERT: B 89 ASP cc_start: 0.8192 (t70) cc_final: 0.7480 (t0) REVERT: A 427 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8380 (mtt) REVERT: A 502 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8002 (mtt90) REVERT: J 89 ASP cc_start: 0.8179 (t70) cc_final: 0.7518 (t0) REVERT: I 502 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.8010 (mtt90) outliers start: 23 outliers final: 10 residues processed: 125 average time/residue: 0.6553 time to fit residues: 93.5749 Evaluate side-chains 114 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 767 ASN Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 1016 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 156 optimal weight: 2.9990 chunk 27 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 287 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.073667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.059098 restraints weight = 44121.597| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.11 r_work: 0.2625 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 24208 Z= 0.212 Angle : 0.530 9.696 32868 Z= 0.279 Chirality : 0.044 0.185 3474 Planarity : 0.003 0.040 4272 Dihedral : 5.796 57.204 3714 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.97 % Rotamer: Outliers : 0.89 % Allowed : 8.49 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 2942 helix: 1.44 (0.21), residues: 670 sheet: 0.42 (0.17), residues: 836 loop : 0.22 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 513 TYR 0.015 0.001 TYR A 422 PHE 0.010 0.001 PHE J 342 TRP 0.011 0.001 TRP J 91 HIS 0.003 0.001 HIS J 302 Details of bonding type rmsd covalent geometry : bond 0.00488 (24188) covalent geometry : angle 0.52004 (32810) SS BOND : bond 0.01252 ( 2) SS BOND : angle 1.41053 ( 4) hydrogen bonds : bond 0.03820 ( 1104) hydrogen bonds : angle 4.47739 ( 3012) glycosidic custom : bond 0.01351 ( 2) glycosidic custom : angle 1.88569 ( 6) link_ALPHA2-6 : bond 0.01024 ( 16) link_ALPHA2-6 : angle 2.65648 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8266 (ptm-80) cc_final: 0.7922 (ttt180) REVERT: B 114 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8386 (mmpt) REVERT: A 427 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8476 (mtt) REVERT: J 7 ARG cc_start: 0.8301 (ptm-80) cc_final: 0.7928 (ttt180) REVERT: J 114 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8358 (mmpt) outliers start: 22 outliers final: 17 residues processed: 114 average time/residue: 0.7379 time to fit residues: 95.8775 Evaluate side-chains 118 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 1016 PHE Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 767 ASN Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 1016 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 121 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 286 optimal weight: 5.9990 chunk 245 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.074516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.059910 restraints weight = 44182.782| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.14 r_work: 0.2648 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24208 Z= 0.139 Angle : 0.490 9.003 32868 Z= 0.259 Chirality : 0.042 0.176 3474 Planarity : 0.003 0.037 4272 Dihedral : 5.585 55.202 3714 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.18 % Favored : 97.76 % Rotamer: Outliers : 0.93 % Allowed : 8.61 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.15), residues: 2942 helix: 1.49 (0.21), residues: 670 sheet: 0.45 (0.17), residues: 834 loop : 0.25 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 502 TYR 0.013 0.001 TYR A 424 PHE 0.010 0.001 PHE A 758 TRP 0.013 0.001 TRP B 91 HIS 0.002 0.001 HIS J 302 Details of bonding type rmsd covalent geometry : bond 0.00311 (24188) covalent geometry : angle 0.47942 (32810) SS BOND : bond 0.01436 ( 2) SS BOND : angle 0.60790 ( 4) hydrogen bonds : bond 0.03404 ( 1104) hydrogen bonds : angle 4.35926 ( 3012) glycosidic custom : bond 0.01385 ( 2) glycosidic custom : angle 1.94572 ( 6) link_ALPHA2-6 : bond 0.01160 ( 16) link_ALPHA2-6 : angle 2.58911 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8249 (ptm-80) cc_final: 0.7925 (ttt180) REVERT: B 89 ASP cc_start: 0.8230 (t70) cc_final: 0.7523 (t0) REVERT: A 427 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8373 (mtt) REVERT: J 7 ARG cc_start: 0.8266 (ptm-80) cc_final: 0.7921 (ttt180) REVERT: J 89 ASP cc_start: 0.8239 (t70) cc_final: 0.7528 (t0) outliers start: 23 outliers final: 13 residues processed: 123 average time/residue: 0.7067 time to fit residues: 100.2855 Evaluate side-chains 119 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 1016 PHE Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 767 ASN Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 1016 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 54 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.072882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.058291 restraints weight = 44340.655| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.11 r_work: 0.2610 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 24208 Z= 0.255 Angle : 0.557 10.150 32868 Z= 0.292 Chirality : 0.045 0.179 3474 Planarity : 0.004 0.048 4272 Dihedral : 5.870 58.264 3714 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 0.85 % Allowed : 8.77 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.15), residues: 2942 helix: 1.38 (0.21), residues: 668 sheet: 0.35 (0.17), residues: 826 loop : 0.09 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 122 TYR 0.017 0.001 TYR I 422 PHE 0.011 0.001 PHE I 526 TRP 0.011 0.001 TRP B 36 HIS 0.003 0.001 HIS J 302 Details of bonding type rmsd covalent geometry : bond 0.00586 (24188) covalent geometry : angle 0.54669 (32810) SS BOND : bond 0.01405 ( 2) SS BOND : angle 1.02911 ( 4) hydrogen bonds : bond 0.04056 ( 1104) hydrogen bonds : angle 4.56501 ( 3012) glycosidic custom : bond 0.01319 ( 2) glycosidic custom : angle 1.93264 ( 6) link_ALPHA2-6 : bond 0.01034 ( 16) link_ALPHA2-6 : angle 2.73226 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8345 (ptm-80) cc_final: 0.8058 (ttt180) REVERT: A 229 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8418 (mtt) REVERT: A 427 MET cc_start: 0.8753 (ttm) cc_final: 0.8465 (mtt) REVERT: A 574 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8757 (t) REVERT: J 7 ARG cc_start: 0.8359 (ptm-80) cc_final: 0.8059 (ttt180) REVERT: I 229 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8415 (mtt) REVERT: I 574 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8753 (t) outliers start: 21 outliers final: 14 residues processed: 115 average time/residue: 0.7451 time to fit residues: 98.1140 Evaluate side-chains 115 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 1016 PHE Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 767 ASN Chi-restraints excluded: chain I residue 876 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 78 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 277 optimal weight: 2.9990 chunk 137 optimal weight: 0.0870 chunk 228 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.073243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.058572 restraints weight = 44385.378| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.13 r_work: 0.2616 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24208 Z= 0.196 Angle : 0.527 9.798 32868 Z= 0.277 Chirality : 0.043 0.176 3474 Planarity : 0.003 0.037 4272 Dihedral : 5.782 56.566 3714 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Rotamer: Outliers : 0.77 % Allowed : 8.89 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 2942 helix: 1.38 (0.21), residues: 668 sheet: 0.34 (0.17), residues: 834 loop : 0.11 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 502 TYR 0.015 0.001 TYR A 422 PHE 0.011 0.001 PHE B 342 TRP 0.012 0.001 TRP J 91 HIS 0.003 0.001 HIS J 302 Details of bonding type rmsd covalent geometry : bond 0.00449 (24188) covalent geometry : angle 0.51734 (32810) SS BOND : bond 0.01201 ( 2) SS BOND : angle 0.84777 ( 4) hydrogen bonds : bond 0.03783 ( 1104) hydrogen bonds : angle 4.51169 ( 3012) glycosidic custom : bond 0.01367 ( 2) glycosidic custom : angle 1.91246 ( 6) link_ALPHA2-6 : bond 0.01082 ( 16) link_ALPHA2-6 : angle 2.64359 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8332 (ptm-80) cc_final: 0.8060 (ttt180) REVERT: A 229 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8421 (mtt) REVERT: A 427 MET cc_start: 0.8730 (ttm) cc_final: 0.8443 (mtt) REVERT: A 574 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8722 (t) REVERT: A 1016 PHE cc_start: 0.8078 (m-80) cc_final: 0.7067 (t80) REVERT: J 7 ARG cc_start: 0.8352 (ptm-80) cc_final: 0.8054 (ttt180) REVERT: I 229 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8429 (mtt) REVERT: I 574 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8718 (t) outliers start: 19 outliers final: 13 residues processed: 117 average time/residue: 0.7084 time to fit residues: 94.9671 Evaluate side-chains 114 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 767 ASN Chi-restraints excluded: chain I residue 876 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 198 optimal weight: 0.8980 chunk 113 optimal weight: 0.0970 chunk 232 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 6 optimal weight: 0.0670 chunk 286 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.075842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.061303 restraints weight = 43738.715| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.12 r_work: 0.2679 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24208 Z= 0.111 Angle : 0.480 9.725 32868 Z= 0.253 Chirality : 0.042 0.191 3474 Planarity : 0.003 0.036 4272 Dihedral : 5.415 59.117 3714 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.48 % Favored : 97.45 % Rotamer: Outliers : 0.61 % Allowed : 9.34 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.16), residues: 2942 helix: 1.51 (0.21), residues: 670 sheet: 0.45 (0.17), residues: 814 loop : 0.24 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 502 TYR 0.011 0.001 TYR A 422 PHE 0.010 0.001 PHE A 758 TRP 0.015 0.001 TRP B 91 HIS 0.003 0.001 HIS J 302 Details of bonding type rmsd covalent geometry : bond 0.00246 (24188) covalent geometry : angle 0.46934 (32810) SS BOND : bond 0.01124 ( 2) SS BOND : angle 1.15876 ( 4) hydrogen bonds : bond 0.03096 ( 1104) hydrogen bonds : angle 4.27926 ( 3012) glycosidic custom : bond 0.01350 ( 2) glycosidic custom : angle 2.02572 ( 6) link_ALPHA2-6 : bond 0.01220 ( 16) link_ALPHA2-6 : angle 2.57315 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5365.05 seconds wall clock time: 93 minutes 4.33 seconds (5584.33 seconds total)