Starting phenix.real_space_refine on Sat Jul 4 21:25:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8aa1_15290/07_2026/8aa1_15290.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aa1_15290/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8aa1_15290/07_2026/8aa1_15290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aa1_15290/07_2026/8aa1_15290.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8aa1_15290/07_2026/8aa1_15290.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8aa1_15290/07_2026/8aa1_15290.cif" model { file = "/net/cci-nas-00/data/ceres_data/8aa1_15290/07_2026/8aa1_15290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aa1_15290/07_2026/8aa1_15290.cif" } 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-dev-6108/lib/python3.11/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 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 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 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 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: 4.50, 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: 1.63 Conformation dependent library (CDL) restraints added in 1.0 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: 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: 0.74 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: 5.31 Time building geometry restraints manager: 2.16 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: 13227 17.05 - 34.10: 621 34.10 - 51.15: 142 51.15 - 68.20: 30 68.20 - 85.25: 6 Dihedral angle restraints: 14026 sinusoidal: 5534 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 14023 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.440 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:9.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 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 : 10.705 85.254 8660 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/Z covalent geometry : bond 0.01056 / 0.53 (24188) covalent geometry : angle 0.54916 / 0.27 (32810) SS BOND : bond 0.00497 / 0.25 ( 2) SS BOND : angle 0.51967 / 0.41 ( 4) hydrogen bonds : bond 0.12276 / 8.67 ( 1104) hydrogen bonds : angle 4.91105 / 3.43 ( 3012) glycosidic custom : bond 0.04027 / 2.02 ( 2) glycosidic custom : angle 3.73430 / 1.80 ( 6) link_ALPHA2-6 : bond 0.08356 / 4.86 ( 16) link_ALPHA2-6 : angle 3.60491 / 2.42 ( 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 : 0.875 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 109 average time/residue: 0.6311 time to fit residues: 79.2028 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 : 0.884 ------------------------------------------------------------------------------- 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... B 43 ASN B 302 HIS A 955 GLN J 43 ASN J 302 HIS I 955 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.078326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.063942 restraints weight = 43872.742| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.13 r_work: 0.2740 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24208 Z= 0.146 Angle : 0.507 8.724 32868 Z= 0.264 Chirality : 0.042 0.148 3474 Planarity : 0.003 0.031 4272 Dihedral : 3.808 45.379 3260 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.55 % 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: 1.18 (0.16), residues: 2942 helix: 1.64 (0.21), residues: 690 sheet: 0.82 (0.18), residues: 814 loop : 0.47 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 513 TYR 0.014 0.001 TYR I 225 PHE 0.011 0.001 PHE A 813 TRP 0.012 0.001 TRP I 878 HIS 0.003 0.001 HIS B 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (24188) covalent geometry : angle 0.49392 / 0.26 (32810) SS BOND : bond 0.00446 / 0.22 ( 2) SS BOND : angle 0.61589 / 0.41 ( 4) hydrogen bonds : bond 0.03541 / 2.38 ( 1104) hydrogen bonds : angle 4.33603 / 3.04 ( 3012) glycosidic custom : bond 0.00795 / 0.40 ( 2) glycosidic custom : angle 2.55510 / 1.82 ( 6) link_ALPHA2-6 : bond 0.01162 / 0.67 ( 16) link_ALPHA2-6 : angle 2.87246 / 1.94 ( 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 127 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.943 Fit side-chains REVERT: A 109 ILE cc_start: 0.8530 (mm) cc_final: 0.8321 (mp) REVERT: A 229 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8586 (mtt) REVERT: A 427 MET cc_start: 0.8557 (ttm) cc_final: 0.8216 (mtt) REVERT: J 126 MET cc_start: 0.9345 (mmp) cc_final: 0.9144 (mmp) REVERT: I 109 ILE cc_start: 0.8536 (mm) cc_final: 0.8331 (mp) REVERT: I 229 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8580 (mtt) outliers start: 14 outliers final: 7 residues processed: 118 average time/residue: 0.7043 time to fit residues: 94.8174 Evaluate side-chains 110 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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: 1.9990 chunk 223 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 279 optimal weight: 0.0060 chunk 119 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 289 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 153 ASN A 309 ASN I 151 ASN I 153 ASN I 309 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.077522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.063068 restraints weight = 44021.602| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.14 r_work: 0.2718 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24208 Z= 0.129 Angle : 0.481 8.377 32868 Z= 0.252 Chirality : 0.042 0.161 3474 Planarity : 0.003 0.034 4272 Dihedral : 3.849 42.810 3260 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.21 % Favored : 97.72 % Rotamer: Outliers : 0.73 % Allowed : 6.67 % Favored : 92.60 % 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: 1.13 (0.16), residues: 2942 helix: 1.61 (0.21), residues: 688 sheet: 0.73 (0.18), residues: 816 loop : 0.47 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 513 TYR 0.014 0.001 TYR A 225 PHE 0.009 0.001 PHE J 342 TRP 0.013 0.001 TRP A 878 HIS 0.004 0.001 HIS J 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (24188) covalent geometry : angle 0.46984 / 0.25 (32810) SS BOND : bond 0.00499 / 0.25 ( 2) SS BOND : angle 1.41380 / 1.04 ( 4) hydrogen bonds : bond 0.03349 / 2.23 ( 1104) hydrogen bonds : angle 4.24715 / 2.99 ( 3012) glycosidic custom : bond 0.01559 / 0.78 ( 2) glycosidic custom : angle 2.43167 / 1.58 ( 6) link_ALPHA2-6 : bond 0.01169 / 0.68 ( 16) link_ALPHA2-6 : angle 2.52881 / 1.70 ( 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 132 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.791 Fit side-chains REVERT: B 126 MET cc_start: 0.9359 (mmp) cc_final: 0.9158 (mmp) REVERT: A 229 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8564 (mtt) REVERT: A 427 MET cc_start: 0.8576 (ttm) cc_final: 0.8226 (mtt) REVERT: J 126 MET cc_start: 0.9383 (mmp) cc_final: 0.9176 (mmp) outliers start: 18 outliers final: 7 residues processed: 121 average time/residue: 0.6380 time to fit residues: 88.3550 Evaluate side-chains 111 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 767 ASN Chi-restraints excluded: chain A residue 1016 PHE Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 516 CYS 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: 4.9990 chunk 94 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 224 optimal weight: 8.9990 chunk 196 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 744 GLN I 151 ASN I 744 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.071919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.057260 restraints weight = 44574.815| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.11 r_work: 0.2588 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.109 24208 Z= 0.369 Angle : 0.644 10.553 32868 Z= 0.338 Chirality : 0.048 0.217 3474 Planarity : 0.005 0.060 4272 Dihedral : 4.468 19.286 3258 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.47 % Favored : 96.46 % Rotamer: Outliers : 1.09 % Allowed : 6.91 % Favored : 92.00 % 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: 1.12 (0.20), residues: 704 sheet: 0.51 (0.17), residues: 822 loop : 0.08 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 513 TYR 0.022 0.002 TYR I 422 PHE 0.015 0.002 PHE I 788 TRP 0.013 0.002 TRP A 535 HIS 0.006 0.002 HIS B 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00859 / 0.37 (24188) covalent geometry : angle 0.63356 / 0.34 (32810) SS BOND : bond 0.00963 / 0.48 ( 2) SS BOND : angle 0.88744 / 0.65 ( 4) hydrogen bonds : bond 0.04751 / 3.17 ( 1104) hydrogen bonds : angle 4.79097 / 3.38 ( 3012) glycosidic custom : bond 0.01375 / 0.69 ( 2) glycosidic custom : angle 2.38607 / 1.49 ( 6) link_ALPHA2-6 : bond 0.00709 / 0.40 ( 16) link_ALPHA2-6 : angle 2.96468 / 1.98 ( 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 131 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.940 Fit side-chains REVERT: A 229 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8433 (mtt) REVERT: A 427 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8494 (mtt) REVERT: A 502 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8078 (mtm-85) REVERT: I 229 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8440 (mtt) REVERT: I 502 ARG cc_start: 0.8453 (mtm-85) cc_final: 0.8092 (mtm-85) outliers start: 27 outliers final: 11 residues processed: 115 average time/residue: 0.6950 time to fit residues: 91.0019 Evaluate side-chains 112 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 427 MET 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 J residue 464 ASP 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 767 ASN Chi-restraints excluded: chain I residue 876 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 183 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 677 GLN I 151 ASN I 677 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.074195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.059597 restraints weight = 43909.246| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.12 r_work: 0.2639 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24208 Z= 0.161 Angle : 0.512 8.887 32868 Z= 0.271 Chirality : 0.043 0.143 3474 Planarity : 0.003 0.036 4272 Dihedral : 4.204 20.230 3258 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.21 % Favored : 97.72 % Rotamer: Outliers : 0.97 % Allowed : 7.76 % Favored : 91.27 % 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: 0.74 (0.15), residues: 2942 helix: 1.35 (0.20), residues: 682 sheet: 0.46 (0.17), residues: 838 loop : 0.21 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 7 TYR 0.014 0.001 TYR I 422 PHE 0.010 0.001 PHE J 301 TRP 0.014 0.001 TRP J 91 HIS 0.003 0.001 HIS I 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (24188) covalent geometry : angle 0.50138 / 0.27 (32810) SS BOND : bond 0.01126 / 0.57 ( 2) SS BOND : angle 1.73066 / 1.33 ( 4) hydrogen bonds : bond 0.03684 / 2.45 ( 1104) hydrogen bonds : angle 4.53145 / 3.20 ( 3012) glycosidic custom : bond 0.01534 / 0.77 ( 2) glycosidic custom : angle 2.48239 / 1.61 ( 6) link_ALPHA2-6 : bond 0.01034 / 0.60 ( 16) link_ALPHA2-6 : angle 2.57776 / 1.73 ( 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 128 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.719 Fit side-chains REVERT: B 7 ARG cc_start: 0.8183 (ptm160) cc_final: 0.7725 (ptp-170) REVERT: A 427 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8438 (mtt) REVERT: J 7 ARG cc_start: 0.8189 (ptm160) cc_final: 0.7729 (ptp-170) REVERT: I 229 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8411 (mtt) outliers start: 24 outliers final: 11 residues processed: 123 average time/residue: 0.6951 time to fit residues: 97.3718 Evaluate side-chains 108 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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 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 767 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.0370 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 259 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.075824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.061338 restraints weight = 43980.062| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.13 r_work: 0.2677 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24208 Z= 0.107 Angle : 0.482 9.754 32868 Z= 0.252 Chirality : 0.042 0.176 3474 Planarity : 0.003 0.036 4272 Dihedral : 3.968 20.984 3258 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.82 % Favored : 97.11 % Rotamer: Outliers : 1.09 % Allowed : 8.00 % Favored : 90.91 % 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: 0.89 (0.16), residues: 2942 helix: 1.51 (0.21), residues: 672 sheet: 0.54 (0.17), residues: 816 loop : 0.32 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 7 TYR 0.012 0.001 TYR B 95 PHE 0.010 0.001 PHE J 301 TRP 0.013 0.001 TRP A 878 HIS 0.002 0.001 HIS J 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (24188) covalent geometry : angle 0.47091 / 0.25 (32810) SS BOND : bond 0.01021 / 0.51 ( 2) SS BOND : angle 0.80082 / 0.55 ( 4) hydrogen bonds : bond 0.03187 / 2.12 ( 1104) hydrogen bonds : angle 4.30743 / 3.05 ( 3012) glycosidic custom : bond 0.01503 / 0.76 ( 2) glycosidic custom : angle 2.42623 / 1.60 ( 6) link_ALPHA2-6 : bond 0.01115 / 0.64 ( 16) link_ALPHA2-6 : angle 2.53405 / 1.71 ( 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: 27 poor density : 106 time to evaluate : 0.809 Fit side-chains REVERT: B 7 ARG cc_start: 0.8135 (ptm160) cc_final: 0.7671 (ptp-170) REVERT: B 89 ASP cc_start: 0.8145 (t70) cc_final: 0.7447 (t0) REVERT: B 114 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8382 (mmpt) REVERT: A 427 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8371 (mtt) REVERT: A 502 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8036 (mtt90) REVERT: J 7 ARG cc_start: 0.8137 (ptm160) cc_final: 0.7669 (ptp-170) REVERT: J 89 ASP cc_start: 0.8139 (t70) cc_final: 0.7436 (t0) REVERT: J 114 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8423 (mmpt) REVERT: I 229 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8400 (mtt) REVERT: I 502 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8035 (mtt90) outliers start: 27 outliers final: 11 residues processed: 123 average time/residue: 0.6256 time to fit residues: 88.9611 Evaluate side-chains 113 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 LYS 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 J residue 114 LYS 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 767 ASN Chi-restraints excluded: chain I residue 876 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 156 optimal weight: 2.9990 chunk 27 optimal weight: 0.0470 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 287 optimal weight: 0.8980 chunk 257 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.075400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.060889 restraints weight = 43905.474| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.12 r_work: 0.2668 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24208 Z= 0.131 Angle : 0.489 8.455 32868 Z= 0.256 Chirality : 0.042 0.151 3474 Planarity : 0.003 0.036 4272 Dihedral : 3.951 21.796 3258 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.48 % Favored : 97.45 % Rotamer: Outliers : 1.01 % Allowed : 8.37 % 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: 0.92 (0.16), residues: 2942 helix: 1.52 (0.21), residues: 674 sheet: 0.56 (0.17), residues: 814 loop : 0.33 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 7 TYR 0.012 0.001 TYR B 95 PHE 0.011 0.001 PHE A 758 TRP 0.011 0.001 TRP J 91 HIS 0.003 0.001 HIS B 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (24188) covalent geometry : angle 0.47859 / 0.25 (32810) SS BOND : bond 0.00951 / 0.48 ( 2) SS BOND : angle 1.30238 / 0.94 ( 4) hydrogen bonds : bond 0.03268 / 2.17 ( 1104) hydrogen bonds : angle 4.29175 / 3.04 ( 3012) glycosidic custom : bond 0.01447 / 0.73 ( 2) glycosidic custom : angle 2.36729 / 1.56 ( 6) link_ALPHA2-6 : bond 0.01049 / 0.60 ( 16) link_ALPHA2-6 : angle 2.55807 / 1.72 ( 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 132 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 89 ASP cc_start: 0.8187 (t70) cc_final: 0.7476 (t0) REVERT: B 114 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8376 (mmpt) REVERT: A 170 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8574 (mt-10) REVERT: A 427 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8364 (mtt) REVERT: A 502 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.8011 (mtt90) REVERT: J 89 ASP cc_start: 0.8176 (t70) cc_final: 0.7462 (t0) REVERT: J 114 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8390 (mmpt) REVERT: I 229 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8386 (mtt) REVERT: I 502 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.8006 (mtt90) outliers start: 25 outliers final: 13 residues processed: 120 average time/residue: 0.6174 time to fit residues: 85.0381 Evaluate side-chains 120 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 178 SER 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 114 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 121 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 179 optimal weight: 0.0670 chunk 78 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 245 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 189 optimal weight: 0.9980 chunk 220 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.076476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.061854 restraints weight = 43745.880| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.14 r_work: 0.2684 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.1575 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= 0.107 Angle : 0.476 8.133 32868 Z= 0.249 Chirality : 0.042 0.175 3474 Planarity : 0.003 0.036 4272 Dihedral : 3.881 24.713 3258 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.52 % Favored : 97.42 % Rotamer: Outliers : 1.01 % Allowed : 8.61 % 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: 0.96 (0.16), residues: 2942 helix: 1.56 (0.21), residues: 674 sheet: 0.58 (0.17), residues: 812 loop : 0.36 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 7 TYR 0.012 0.001 TYR I 422 PHE 0.010 0.001 PHE I 758 TRP 0.013 0.001 TRP J 91 HIS 0.003 0.001 HIS B 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (24188) covalent geometry : angle 0.46539 / 0.25 (32810) SS BOND : bond 0.00897 / 0.45 ( 2) SS BOND : angle 0.53125 / 0.43 ( 4) hydrogen bonds : bond 0.03076 / 2.05 ( 1104) hydrogen bonds : angle 4.21229 / 2.99 ( 3012) glycosidic custom : bond 0.01451 / 0.73 ( 2) glycosidic custom : angle 2.37170 / 1.57 ( 6) link_ALPHA2-6 : bond 0.01094 / 0.63 ( 16) link_ALPHA2-6 : angle 2.52312 / 1.70 ( 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 130 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8134 (ptm160) cc_final: 0.7581 (ptp-170) REVERT: A 427 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8376 (mtt) REVERT: A 502 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.8019 (mtt90) REVERT: J 7 ARG cc_start: 0.8139 (ptm160) cc_final: 0.7583 (ptp-170) REVERT: I 229 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8371 (mtt) REVERT: I 502 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.8015 (mtt90) outliers start: 25 outliers final: 9 residues processed: 117 average time/residue: 0.6315 time to fit residues: 85.3520 Evaluate side-chains 111 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 LEU 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 54 optimal weight: 7.9990 chunk 273 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 163 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 ASN A 152 ASN I 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.060054 restraints weight = 44022.973| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.13 r_work: 0.2654 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24208 Z= 0.165 Angle : 0.504 9.268 32868 Z= 0.263 Chirality : 0.043 0.162 3474 Planarity : 0.003 0.036 4272 Dihedral : 3.985 24.272 3258 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.82 % Favored : 97.11 % Rotamer: Outliers : 0.77 % Allowed : 8.69 % Favored : 90.54 % 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: 0.89 (0.16), residues: 2942 helix: 1.49 (0.21), residues: 674 sheet: 0.51 (0.17), residues: 818 loop : 0.34 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 7 TYR 0.014 0.001 TYR I 422 PHE 0.010 0.001 PHE J 342 TRP 0.010 0.001 TRP B 91 HIS 0.003 0.001 HIS B 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (24188) covalent geometry : angle 0.49371 / 0.26 (32810) SS BOND : bond 0.01221 / 0.61 ( 2) SS BOND : angle 0.88636 / 0.70 ( 4) hydrogen bonds : bond 0.03459 / 2.30 ( 1104) hydrogen bonds : angle 4.30686 / 3.05 ( 3012) glycosidic custom : bond 0.01449 / 0.73 ( 2) glycosidic custom : angle 2.36083 / 1.54 ( 6) link_ALPHA2-6 : bond 0.00988 / 0.57 ( 16) link_ALPHA2-6 : angle 2.61321 / 1.75 ( 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 123 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8240 (ptm160) cc_final: 0.7668 (ptp-170) REVERT: B 89 ASP cc_start: 0.8261 (t70) cc_final: 0.7540 (t0) REVERT: A 427 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8410 (mtt) REVERT: J 7 ARG cc_start: 0.8232 (ptm160) cc_final: 0.7660 (ptp-170) REVERT: J 89 ASP cc_start: 0.8249 (t70) cc_final: 0.7524 (t0) REVERT: I 229 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8356 (mtt) outliers start: 19 outliers final: 12 residues processed: 116 average time/residue: 0.6372 time to fit residues: 84.7239 Evaluate side-chains 117 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 178 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 78 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 267 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 277 optimal weight: 6.9990 chunk 137 optimal weight: 0.4980 chunk 228 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.072711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.058024 restraints weight = 44593.459| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.13 r_work: 0.2599 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 24208 Z= 0.252 Angle : 0.564 10.453 32868 Z= 0.295 Chirality : 0.045 0.190 3474 Planarity : 0.004 0.051 4272 Dihedral : 4.265 24.158 3258 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.77 % Rotamer: Outliers : 0.77 % Allowed : 9.05 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.15), residues: 2942 helix: 1.40 (0.21), residues: 670 sheet: 0.36 (0.17), residues: 838 loop : 0.19 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 7 TYR 0.018 0.001 TYR A 422 PHE 0.012 0.001 PHE J 342 TRP 0.011 0.001 TRP B 36 HIS 0.003 0.001 HIS B 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 (24188) covalent geometry : angle 0.55328 / 0.29 (32810) SS BOND : bond 0.01483 / 0.74 ( 2) SS BOND : angle 0.99629 / 0.77 ( 4) hydrogen bonds : bond 0.04071 / 2.71 ( 1104) hydrogen bonds : angle 4.55055 / 3.22 ( 3012) glycosidic custom : bond 0.01464 / 0.73 ( 2) glycosidic custom : angle 2.41494 / 1.56 ( 6) link_ALPHA2-6 : bond 0.00865 / 0.49 ( 16) link_ALPHA2-6 : angle 2.75073 / 1.83 ( 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 117 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.634 Fit side-chains REVERT: B 7 ARG cc_start: 0.8411 (ptm160) cc_final: 0.7879 (ptp-170) REVERT: A 427 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8499 (mtt) REVERT: A 1016 PHE cc_start: 0.8075 (m-80) cc_final: 0.7184 (t80) REVERT: J 7 ARG cc_start: 0.8411 (ptm160) cc_final: 0.7873 (ptp-170) REVERT: I 229 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8455 (mtt) outliers start: 19 outliers final: 12 residues processed: 111 average time/residue: 0.6489 time to fit residues: 82.8624 Evaluate side-chains 110 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 178 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 198 optimal weight: 1.9990 chunk 113 optimal weight: 0.0370 chunk 232 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 overall best weight: 1.1064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.074863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.060231 restraints weight = 43887.575| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.13 r_work: 0.2655 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.1780 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= 0.137 Angle : 0.502 9.628 32868 Z= 0.263 Chirality : 0.042 0.177 3474 Planarity : 0.003 0.035 4272 Dihedral : 4.086 24.145 3258 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.24 % Favored : 97.69 % Rotamer: Outliers : 0.73 % Allowed : 9.09 % Favored : 90.18 % 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: 0.76 (0.15), residues: 2942 helix: 1.45 (0.21), residues: 670 sheet: 0.42 (0.17), residues: 834 loop : 0.24 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 7 TYR 0.014 0.001 TYR A 422 PHE 0.010 0.001 PHE J 342 TRP 0.014 0.001 TRP B 91 HIS 0.002 0.001 HIS B 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (24188) covalent geometry : angle 0.49161 / 0.26 (32810) SS BOND : bond 0.01228 / 0.62 ( 2) SS BOND : angle 1.16616 / 0.87 ( 4) hydrogen bonds : bond 0.03380 / 2.25 ( 1104) hydrogen bonds : angle 4.37966 / 3.11 ( 3012) glycosidic custom : bond 0.01460 / 0.73 ( 2) glycosidic custom : angle 2.43128 / 1.58 ( 6) link_ALPHA2-6 : bond 0.01068 / 0.61 ( 16) link_ALPHA2-6 : angle 2.54789 / 1.71 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5285.98 seconds wall clock time: 91 minutes 42.80 seconds (5502.80 seconds total)