Starting phenix.real_space_refine on Fri Jun 20 10:02:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aa1_15290/06_2025/8aa1_15290.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aa1_15290/06_2025/8aa1_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_15290/06_2025/8aa1_15290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aa1_15290/06_2025/8aa1_15290.map" model { file = "/net/cci-nas-00/data/ceres_data/8aa1_15290/06_2025/8aa1_15290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aa1_15290/06_2025/8aa1_15290.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23634 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4432 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 7260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7260 Classifications: {'peptide': 924} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 32, 'TRANS': 891} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4432 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 7260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7260 Classifications: {'peptide': 924} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 32, 'TRANS': 891} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FRU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FRU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 78 Unusual residues: {'FRU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 78 Unusual residues: {'FRU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.70, per 1000 atoms: 0.58 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: 6.48 Conformation dependent library (CDL) restraints added in 3.0 seconds 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5360 Finding SS restraints... Secondary structure from input PDB file: 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: 2.74 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: 9.35 Time building geometry restraints manager: 7.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7774 1.34 - 1.46: 6037 1.46 - 1.58: 10163 1.58 - 1.70: 66 1.70 - 1.81: 148 Bond restraints: 24188 Sorted by residual: bond pdb=" C2 FRU C 7 " pdb=" O5 FRU C 7 " ideal model delta sigma weight residual 1.412 1.643 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C2 FRU L 4 " pdb=" O5 FRU L 4 " ideal model delta sigma weight residual 1.412 1.642 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2 FRU K 3 " pdb=" O5 FRU K 3 " ideal model delta sigma weight residual 1.412 1.642 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2 FRU L 3 " pdb=" O5 FRU L 3 " ideal model delta sigma weight residual 1.412 1.641 -0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2 FRU D 4 " pdb=" O5 FRU D 4 " ideal model delta sigma weight residual 1.412 1.641 -0.229 2.00e-02 2.50e+03 1.32e+02 ... (remaining 24183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 32369 2.00 - 3.99: 323 3.99 - 5.99: 102 5.99 - 7.98: 12 7.98 - 9.98: 4 Bond angle restraints: 32810 Sorted by residual: angle pdb=" C CYS B 298 " pdb=" N CYS B 299 " pdb=" CA CYS B 299 " ideal model delta sigma weight residual 121.54 129.62 -8.08 1.91e+00 2.74e-01 1.79e+01 angle pdb=" C CYS J 298 " pdb=" N CYS J 299 " pdb=" CA CYS J 299 " ideal model delta sigma weight residual 121.54 129.58 -8.04 1.91e+00 2.74e-01 1.77e+01 angle pdb=" CA LYS A 318 " pdb=" CB LYS A 318 " pdb=" CG LYS A 318 " ideal model delta sigma weight residual 114.10 120.88 -6.78 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA LYS I 318 " pdb=" CB LYS I 318 " pdb=" CG LYS I 318 " ideal model delta sigma weight residual 114.10 120.88 -6.78 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CB MET I 427 " pdb=" CG MET I 427 " pdb=" SD MET I 427 " ideal model delta sigma weight residual 112.70 102.72 9.98 3.00e+00 1.11e-01 1.11e+01 ... (remaining 32805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 13441 17.05 - 34.10: 727 34.10 - 51.15: 232 51.15 - 68.20: 74 68.20 - 85.25: 8 Dihedral angle restraints: 14482 sinusoidal: 5990 harmonic: 8492 Sorted by residual: dihedral pdb=" CA ARG J 7 " pdb=" C ARG J 7 " pdb=" N GLN J 8 " pdb=" CA GLN J 8 " ideal model delta harmonic sigma weight residual 180.00 -160.73 -19.27 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ARG B 7 " pdb=" C ARG B 7 " pdb=" N GLN B 8 " pdb=" CA GLN B 8 " ideal model delta harmonic sigma weight residual -180.00 -160.73 -19.27 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA CYS B 387 " pdb=" C CYS B 387 " pdb=" N ASP B 388 " pdb=" CA ASP B 388 " ideal model delta harmonic sigma weight residual 180.00 -161.83 -18.17 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 14479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2380 0.038 - 0.077: 793 0.077 - 0.115: 244 0.115 - 0.153: 53 0.153 - 0.192: 4 Chirality restraints: 3474 Sorted by residual: chirality pdb=" C2 FRU K 7 " pdb=" O1 FRU K 3 " pdb=" C1 FRU K 7 " pdb=" O5 FRU K 7 " both_signs ideal model delta sigma weight residual False 2.60 2.79 -0.19 2.00e-02 2.50e+03 9.19e+01 chirality pdb=" C2 FRU C 7 " pdb=" O1 FRU C 3 " pdb=" C1 FRU C 7 " pdb=" O5 FRU C 7 " both_signs ideal model delta sigma weight residual False 2.60 2.79 -0.19 2.00e-02 2.50e+03 9.04e+01 chirality pdb=" C2 FRU L 4 " pdb=" O6 FRU L 3 " pdb=" C1 FRU L 4 " pdb=" O5 FRU L 4 " both_signs ideal model delta sigma weight residual False 2.60 2.68 -0.08 2.00e-02 2.50e+03 1.41e+01 ... (remaining 3471 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 592 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO A 593 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 593 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 593 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE I 592 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.89e+00 pdb=" N PRO I 593 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO I 593 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 593 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 530 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO I 531 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO I 531 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 531 " 0.016 5.00e-02 4.00e+02 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 335 2.63 - 3.20: 20526 3.20 - 3.76: 37434 3.76 - 4.33: 54951 4.33 - 4.90: 90820 Nonbonded interactions: 204066 Sorted by model distance: nonbonded pdb=" OD1 ASN J 401 " pdb="MG MG J 601 " model vdw 2.061 2.170 nonbonded pdb=" OD1 ASN B 401 " pdb="MG MG B 601 " model vdw 2.062 2.170 nonbonded pdb=" OD1 ASN A 841 " pdb="MG MG A1101 " model vdw 2.107 2.170 nonbonded pdb=" OD1 ASN I 841 " pdb="MG MG I1101 " model vdw 2.107 2.170 nonbonded pdb=" OD2 ASP A 848 " pdb="MG MG A1101 " model vdw 2.108 2.170 ... (remaining 204061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.13 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.960 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 54.880 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.130 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:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.231 24208 Z= 0.539 Angle : 0.568 9.977 32868 Z= 0.271 Chirality : 0.043 0.192 3474 Planarity : 0.003 0.034 4272 Dihedral : 12.372 85.254 9116 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.56 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (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 TRP 0.012 0.001 TRP J 91 HIS 0.002 0.000 HIS J 302 PHE 0.010 0.001 PHE J 301 TYR 0.011 0.001 TYR I 225 ARG 0.004 0.000 ARG J 7 Details of bonding type rmsd link_ALPHA2-6 : bond 0.08356 ( 16) link_ALPHA2-6 : angle 3.60491 ( 48) hydrogen bonds : bond 0.12276 ( 1104) hydrogen bonds : angle 4.91105 ( 3012) SS BOND : bond 0.00497 ( 2) SS BOND : angle 0.51967 ( 4) glycosidic custom : bond 0.04027 ( 2) glycosidic custom : angle 3.73430 ( 6) covalent geometry : bond 0.01056 (24188) covalent geometry : angle 0.54916 (32810) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 2.518 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 109 average time/residue: 1.5498 time to fit residues: 195.1635 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 : 3.195 ------------------------------------------------------------------------------- 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 248 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 230 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 140 optimal weight: 0.2980 chunk 171 optimal weight: 6.9990 chunk 266 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 302 HIS A 955 GLN J 302 HIS I 955 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.079650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.065408 restraints weight = 43728.122| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.13 r_work: 0.2770 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24208 Z= 0.116 Angle : 0.499 8.411 32868 Z= 0.257 Chirality : 0.042 0.154 3474 Planarity : 0.003 0.031 4272 Dihedral : 7.327 59.859 3716 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.28 % Favored : 97.65 % Rotamer: Outliers : 0.44 % Allowed : 6.43 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.16), residues: 2942 helix: 1.67 (0.21), residues: 690 sheet: 0.84 (0.18), residues: 814 loop : 0.49 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 878 HIS 0.002 0.001 HIS B 302 PHE 0.010 0.001 PHE A 813 TYR 0.013 0.001 TYR J 33 ARG 0.003 0.000 ARG I 513 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01172 ( 16) link_ALPHA2-6 : angle 3.00689 ( 48) hydrogen bonds : bond 0.03288 ( 1104) hydrogen bonds : angle 4.26831 ( 3012) SS BOND : bond 0.00395 ( 2) SS BOND : angle 0.57603 ( 4) glycosidic custom : bond 0.01286 ( 2) glycosidic custom : angle 1.87564 ( 6) covalent geometry : bond 0.00254 (24188) covalent geometry : angle 0.48507 (32810) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 2.364 Fit side-chains REVERT: A 280 LYS cc_start: 0.6583 (mmtt) cc_final: 0.5965 (tptp) REVERT: A 427 MET cc_start: 0.8524 (ttm) cc_final: 0.8171 (mtt) REVERT: A 515 ASP cc_start: 0.8665 (m-30) cc_final: 0.8455 (m-30) REVERT: I 280 LYS cc_start: 0.6606 (mmtt) cc_final: 0.5955 (tptp) REVERT: I 515 ASP cc_start: 0.8660 (m-30) cc_final: 0.8452 (m-30) outliers start: 11 outliers final: 5 residues processed: 123 average time/residue: 1.8917 time to fit residues: 266.2667 Evaluate side-chains 108 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 516 CYS 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 236 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 118 optimal weight: 0.2980 chunk 200 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3105 r_free = 0.3105 target = 0.077306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.062843 restraints weight = 43612.306| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.12 r_work: 0.2711 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24208 Z= 0.141 Angle : 0.490 9.133 32868 Z= 0.258 Chirality : 0.042 0.143 3474 Planarity : 0.003 0.035 4272 Dihedral : 5.636 54.956 3716 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.41 % Favored : 97.52 % Rotamer: Outliers : 0.89 % Allowed : 6.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.16), residues: 2942 helix: 1.64 (0.21), residues: 686 sheet: 0.74 (0.18), residues: 804 loop : 0.47 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 878 HIS 0.005 0.001 HIS B 302 PHE 0.010 0.001 PHE B 342 TYR 0.014 0.001 TYR A 225 ARG 0.008 0.000 ARG I 502 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01316 ( 16) link_ALPHA2-6 : angle 2.59554 ( 48) hydrogen bonds : bond 0.03438 ( 1104) hydrogen bonds : angle 4.25230 ( 3012) SS BOND : bond 0.00970 ( 2) SS BOND : angle 0.51917 ( 4) glycosidic custom : bond 0.01508 ( 2) glycosidic custom : angle 1.92237 ( 6) covalent geometry : bond 0.00315 (24188) covalent geometry : angle 0.47984 (32810) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 2.736 Fit side-chains REVERT: A 109 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8324 (mp) REVERT: A 229 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8554 (mtt) REVERT: A 427 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8307 (mtt) REVERT: A 502 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7852 (mtt90) REVERT: I 109 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8336 (mp) REVERT: I 229 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8546 (mtt) outliers start: 22 outliers final: 9 residues processed: 118 average time/residue: 1.6495 time to fit residues: 221.9495 Evaluate side-chains 116 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 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 1016 PHE Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 516 CYS Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 767 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 110 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 243 optimal weight: 4.9990 chunk 234 optimal weight: 0.7980 chunk 282 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.074682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.060087 restraints weight = 44651.778| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.13 r_work: 0.2648 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 24208 Z= 0.207 Angle : 0.527 9.352 32868 Z= 0.277 Chirality : 0.044 0.153 3474 Planarity : 0.004 0.039 4272 Dihedral : 5.691 55.392 3714 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.99 % Favored : 96.94 % Rotamer: Outliers : 0.97 % Allowed : 7.32 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.16), residues: 2942 helix: 1.44 (0.20), residues: 684 sheet: 0.61 (0.17), residues: 836 loop : 0.35 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 91 HIS 0.003 0.001 HIS B 302 PHE 0.011 0.001 PHE B 493 TYR 0.016 0.001 TYR A 422 ARG 0.004 0.000 ARG J 7 Details of bonding type rmsd link_ALPHA2-6 : bond 0.00989 ( 16) link_ALPHA2-6 : angle 2.68658 ( 48) hydrogen bonds : bond 0.03803 ( 1104) hydrogen bonds : angle 4.42141 ( 3012) SS BOND : bond 0.01029 ( 2) SS BOND : angle 0.71289 ( 4) glycosidic custom : bond 0.01313 ( 2) glycosidic custom : angle 1.78317 ( 6) covalent geometry : bond 0.00479 (24188) covalent geometry : angle 0.51644 (32810) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 2.490 Fit side-chains REVERT: B 89 ASP cc_start: 0.8289 (t70) cc_final: 0.7645 (t0) REVERT: A 109 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8402 (mp) REVERT: A 229 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8461 (mtt) REVERT: A 427 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8469 (mtt) REVERT: J 89 ASP cc_start: 0.8259 (t70) cc_final: 0.7697 (t0) REVERT: I 109 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8407 (mp) REVERT: I 229 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8481 (mtt) REVERT: I 427 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8452 (ttm) REVERT: I 502 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.7934 (mtt90) outliers start: 24 outliers final: 7 residues processed: 120 average time/residue: 1.5345 time to fit residues: 212.4015 Evaluate side-chains 117 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 2.547 ------------------------------------------------------------------------------- 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 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 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 427 MET Chi-restraints excluded: chain I residue 767 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 9 optimal weight: 0.6980 chunk 224 optimal weight: 7.9990 chunk 226 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 GLN A 744 GLN J 43 ASN I 677 GLN I 744 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.073729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.059140 restraints weight = 44362.750| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.11 r_work: 0.2630 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 24208 Z= 0.222 Angle : 0.537 9.542 32868 Z= 0.284 Chirality : 0.044 0.178 3474 Planarity : 0.004 0.038 4272 Dihedral : 5.905 57.984 3714 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 1.33 % Allowed : 7.60 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.15), residues: 2942 helix: 1.39 (0.20), residues: 682 sheet: 0.50 (0.17), residues: 836 loop : 0.25 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 91 HIS 0.003 0.001 HIS J 302 PHE 0.010 0.001 PHE J 342 TYR 0.016 0.001 TYR I 422 ARG 0.005 0.001 ARG J 7 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01039 ( 16) link_ALPHA2-6 : angle 2.67072 ( 48) hydrogen bonds : bond 0.03887 ( 1104) hydrogen bonds : angle 4.51441 ( 3012) SS BOND : bond 0.01051 ( 2) SS BOND : angle 0.99992 ( 4) glycosidic custom : bond 0.01485 ( 2) glycosidic custom : angle 1.91566 ( 6) covalent geometry : bond 0.00512 (24188) covalent geometry : angle 0.52707 (32810) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 2.540 Fit side-chains REVERT: B 7 ARG cc_start: 0.8239 (ptm160) cc_final: 0.7730 (ptp-170) REVERT: A 229 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8403 (mtt) REVERT: A 427 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8426 (mtt) REVERT: A 502 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.7993 (mtt90) REVERT: J 7 ARG cc_start: 0.8242 (ptm160) cc_final: 0.7732 (ptp-170) REVERT: J 114 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8327 (mmpt) REVERT: I 229 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8402 (mtt) outliers start: 33 outliers final: 14 residues processed: 124 average time/residue: 1.6098 time to fit residues: 228.0887 Evaluate side-chains 114 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 1016 PHE Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 767 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 179 optimal weight: 0.1980 chunk 230 optimal weight: 2.9990 chunk 132 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.074266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.059697 restraints weight = 44012.694| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.11 r_work: 0.2640 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1686 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= 0.169 Angle : 0.511 9.133 32868 Z= 0.268 Chirality : 0.043 0.148 3474 Planarity : 0.003 0.036 4272 Dihedral : 5.767 56.105 3714 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.25 % Rotamer: Outliers : 1.01 % Allowed : 7.84 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 2942 helix: 1.42 (0.20), residues: 680 sheet: 0.45 (0.17), residues: 836 loop : 0.24 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 91 HIS 0.003 0.001 HIS J 302 PHE 0.010 0.001 PHE B 342 TYR 0.014 0.001 TYR A 422 ARG 0.004 0.000 ARG I 502 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01128 ( 16) link_ALPHA2-6 : angle 2.62964 ( 48) hydrogen bonds : bond 0.03637 ( 1104) hydrogen bonds : angle 4.44884 ( 3012) SS BOND : bond 0.00695 ( 2) SS BOND : angle 0.88983 ( 4) glycosidic custom : bond 0.01485 ( 2) glycosidic custom : angle 1.94685 ( 6) covalent geometry : bond 0.00384 (24188) covalent geometry : angle 0.50023 (32810) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 2.902 Fit side-chains REVERT: B 7 ARG cc_start: 0.8229 (ptm160) cc_final: 0.7724 (ptp-170) REVERT: B 89 ASP cc_start: 0.8270 (t70) cc_final: 0.7654 (t0) REVERT: A 229 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8374 (mtt) REVERT: A 427 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8418 (mtt) REVERT: J 7 ARG cc_start: 0.8238 (ptm160) cc_final: 0.7729 (ptp-170) REVERT: J 89 ASP cc_start: 0.8258 (t70) cc_final: 0.7643 (t0) REVERT: I 229 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8418 (mtt) outliers start: 25 outliers final: 17 residues processed: 122 average time/residue: 1.6503 time to fit residues: 232.3585 Evaluate side-chains 118 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 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 203 TYR Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 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 181 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 282 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.072490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.057894 restraints weight = 44553.023| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.11 r_work: 0.2603 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 24208 Z= 0.283 Angle : 0.576 9.726 32868 Z= 0.302 Chirality : 0.045 0.194 3474 Planarity : 0.004 0.047 4272 Dihedral : 6.012 56.749 3714 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 1.05 % Allowed : 8.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.15), residues: 2942 helix: 1.31 (0.20), residues: 680 sheet: 0.34 (0.17), residues: 826 loop : 0.07 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 36 HIS 0.004 0.001 HIS J 302 PHE 0.012 0.002 PHE A 526 TYR 0.018 0.002 TYR A 422 ARG 0.004 0.001 ARG I 513 Details of bonding type rmsd link_ALPHA2-6 : bond 0.00935 ( 16) link_ALPHA2-6 : angle 2.72594 ( 48) hydrogen bonds : bond 0.04201 ( 1104) hydrogen bonds : angle 4.64001 ( 3012) SS BOND : bond 0.01432 ( 2) SS BOND : angle 1.09558 ( 4) glycosidic custom : bond 0.01433 ( 2) glycosidic custom : angle 1.92308 ( 6) covalent geometry : bond 0.00655 (24188) covalent geometry : angle 0.56583 (32810) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 3.960 Fit side-chains REVERT: B 7 ARG cc_start: 0.8413 (ptm160) cc_final: 0.7936 (ptp-170) REVERT: B 114 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8286 (mmpt) REVERT: A 229 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8401 (mtt) REVERT: A 427 MET cc_start: 0.8754 (ttm) cc_final: 0.8494 (mtt) REVERT: A 574 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8749 (t) REVERT: J 7 ARG cc_start: 0.8423 (ptm160) cc_final: 0.7943 (ptp-170) REVERT: J 114 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8386 (mmpt) REVERT: I 229 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8397 (mtt) REVERT: I 574 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8752 (t) outliers start: 26 outliers final: 15 residues processed: 111 average time/residue: 1.6901 time to fit residues: 215.2337 Evaluate side-chains 115 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 574 THR 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 J residue 203 TYR Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 574 THR 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 76 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 202 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.074437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.059924 restraints weight = 43802.270| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.11 r_work: 0.2645 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1805 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= 0.150 Angle : 0.503 8.899 32868 Z= 0.265 Chirality : 0.042 0.171 3474 Planarity : 0.003 0.036 4272 Dihedral : 5.771 58.040 3714 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.28 % Favored : 97.65 % Rotamer: Outliers : 0.89 % Allowed : 8.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 2942 helix: 1.44 (0.21), residues: 668 sheet: 0.45 (0.17), residues: 814 loop : 0.14 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 91 HIS 0.002 0.001 HIS J 302 PHE 0.009 0.001 PHE A 758 TYR 0.013 0.001 TYR A 422 ARG 0.005 0.000 ARG I 502 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01172 ( 16) link_ALPHA2-6 : angle 2.59441 ( 48) hydrogen bonds : bond 0.03511 ( 1104) hydrogen bonds : angle 4.44164 ( 3012) SS BOND : bond 0.00776 ( 2) SS BOND : angle 0.56740 ( 4) glycosidic custom : bond 0.01450 ( 2) glycosidic custom : angle 1.94103 ( 6) covalent geometry : bond 0.00337 (24188) covalent geometry : angle 0.49272 (32810) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 2.903 Fit side-chains REVERT: B 7 ARG cc_start: 0.8307 (ptm160) cc_final: 0.7802 (ptp-170) REVERT: B 89 ASP cc_start: 0.8240 (t70) cc_final: 0.7534 (t0) REVERT: B 114 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8360 (mmpt) REVERT: A 229 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8393 (mtt) REVERT: A 427 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8422 (mtt) REVERT: A 574 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8725 (t) REVERT: J 7 ARG cc_start: 0.8315 (ptm160) cc_final: 0.7818 (ptp-170) REVERT: J 89 ASP cc_start: 0.8235 (t70) cc_final: 0.7525 (t0) REVERT: J 114 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8392 (mmpt) REVERT: I 229 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8382 (mtt) REVERT: I 502 ARG cc_start: 0.8457 (mtm-85) cc_final: 0.8090 (mtm-85) REVERT: I 574 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8726 (t) outliers start: 22 outliers final: 10 residues processed: 114 average time/residue: 1.6862 time to fit residues: 221.8515 Evaluate side-chains 117 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 574 THR 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 J residue 203 TYR Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 767 ASN Chi-restraints excluded: chain I residue 876 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 166 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 chunk 287 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 278 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.074572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.060044 restraints weight = 43922.422| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.11 r_work: 0.2648 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24208 Z= 0.150 Angle : 0.502 9.481 32868 Z= 0.264 Chirality : 0.042 0.198 3474 Planarity : 0.003 0.036 4272 Dihedral : 5.623 58.962 3714 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.75 % Favored : 97.18 % Rotamer: Outliers : 0.93 % Allowed : 8.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 2942 helix: 1.45 (0.21), residues: 670 sheet: 0.43 (0.17), residues: 818 loop : 0.19 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 91 HIS 0.003 0.001 HIS J 302 PHE 0.010 0.001 PHE B 342 TYR 0.013 0.001 TYR J 95 ARG 0.004 0.000 ARG I 502 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01145 ( 16) link_ALPHA2-6 : angle 2.60648 ( 48) hydrogen bonds : bond 0.03473 ( 1104) hydrogen bonds : angle 4.38875 ( 3012) SS BOND : bond 0.01255 ( 2) SS BOND : angle 1.02496 ( 4) glycosidic custom : bond 0.01351 ( 2) glycosidic custom : angle 1.93170 ( 6) covalent geometry : bond 0.00338 (24188) covalent geometry : angle 0.49186 (32810) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 2.977 Fit side-chains REVERT: B 7 ARG cc_start: 0.8244 (ptm160) cc_final: 0.7737 (ptp-170) REVERT: B 89 ASP cc_start: 0.8243 (t70) cc_final: 0.7536 (t0) REVERT: B 114 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8402 (mmpt) REVERT: A 229 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8399 (mtt) REVERT: A 427 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8441 (mtt) REVERT: A 574 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8731 (t) REVERT: J 7 ARG cc_start: 0.8270 (ptm160) cc_final: 0.7755 (ptp-170) REVERT: J 89 ASP cc_start: 0.8232 (t70) cc_final: 0.7521 (t0) REVERT: I 229 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8392 (mtt) REVERT: I 574 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8732 (t) outliers start: 23 outliers final: 14 residues processed: 118 average time/residue: 2.1796 time to fit residues: 298.0891 Evaluate side-chains 121 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 3.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 767 ASN Chi-restraints excluded: chain I residue 876 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 246 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 chunk 192 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.074876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.060195 restraints weight = 43954.697| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.13 r_work: 0.2656 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24208 Z= 0.139 Angle : 0.495 9.660 32868 Z= 0.260 Chirality : 0.042 0.189 3474 Planarity : 0.003 0.036 4272 Dihedral : 5.499 59.896 3714 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.35 % Favored : 97.59 % Rotamer: Outliers : 0.81 % Allowed : 9.05 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 2942 helix: 1.48 (0.21), residues: 670 sheet: 0.49 (0.17), residues: 796 loop : 0.20 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 91 HIS 0.003 0.001 HIS J 302 PHE 0.009 0.001 PHE J 342 TYR 0.012 0.001 TYR J 95 ARG 0.004 0.000 ARG I 502 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01163 ( 16) link_ALPHA2-6 : angle 2.60045 ( 48) hydrogen bonds : bond 0.03370 ( 1104) hydrogen bonds : angle 4.34120 ( 3012) SS BOND : bond 0.01116 ( 2) SS BOND : angle 1.23688 ( 4) glycosidic custom : bond 0.01326 ( 2) glycosidic custom : angle 1.95033 ( 6) covalent geometry : bond 0.00313 (24188) covalent geometry : angle 0.48405 (32810) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 2.718 Fit side-chains REVERT: B 7 ARG cc_start: 0.8239 (ptm160) cc_final: 0.7726 (ptp-170) REVERT: B 89 ASP cc_start: 0.8219 (t70) cc_final: 0.7499 (t0) REVERT: A 229 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8351 (mtt) REVERT: A 427 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8404 (mtt) REVERT: A 502 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.8054 (mtt90) REVERT: A 574 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8743 (t) REVERT: A 614 ASP cc_start: 0.8390 (t0) cc_final: 0.8171 (t0) REVERT: J 7 ARG cc_start: 0.8239 (ptm160) cc_final: 0.8011 (ptm-80) REVERT: J 89 ASP cc_start: 0.8208 (t70) cc_final: 0.7484 (t0) REVERT: I 229 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8337 (mtt) REVERT: I 574 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8746 (t) REVERT: I 614 ASP cc_start: 0.8403 (t0) cc_final: 0.8175 (t0) outliers start: 20 outliers final: 15 residues processed: 120 average time/residue: 1.5240 time to fit residues: 210.1320 Evaluate side-chains 122 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 1016 PHE Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 767 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 233 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 187 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.075022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.060367 restraints weight = 43800.889| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.13 r_work: 0.2659 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24208 Z= 0.135 Angle : 0.492 9.860 32868 Z= 0.258 Chirality : 0.042 0.184 3474 Planarity : 0.003 0.036 4272 Dihedral : 5.413 59.674 3714 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.65 % Favored : 97.28 % Rotamer: Outliers : 0.93 % Allowed : 8.85 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 2942 helix: 1.50 (0.21), residues: 670 sheet: 0.46 (0.17), residues: 800 loop : 0.23 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 91 HIS 0.003 0.001 HIS J 302 PHE 0.009 0.001 PHE A 758 TYR 0.013 0.001 TYR J 95 ARG 0.005 0.000 ARG I 502 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01163 ( 16) link_ALPHA2-6 : angle 2.59598 ( 48) hydrogen bonds : bond 0.03327 ( 1104) hydrogen bonds : angle 4.31700 ( 3012) SS BOND : bond 0.01087 ( 2) SS BOND : angle 1.18817 ( 4) glycosidic custom : bond 0.01297 ( 2) glycosidic custom : angle 1.96593 ( 6) covalent geometry : bond 0.00302 (24188) covalent geometry : angle 0.48164 (32810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12420.14 seconds wall clock time: 218 minutes 55.57 seconds (13135.57 seconds total)