Starting phenix.real_space_refine on Mon Jul 6 05:13:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8aa0_15289/07_2026/8aa0_15289.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aa0_15289/07_2026/8aa0_15289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8aa0_15289/07_2026/8aa0_15289.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8aa0_15289/07_2026/8aa0_15289.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8aa0_15289/07_2026/8aa0_15289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aa0_15289/07_2026/8aa0_15289.map" model { file = "/net/cci-nas-00/data/ceres_data/8aa0_15289/07_2026/8aa0_15289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aa0_15289/07_2026/8aa0_15289.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 4 5.21 5 S 128 5.16 5 C 20892 2.51 5 N 5520 2.21 5 O 6514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33058 Number of models: 1 Model: "" Number of chains: 16 Chain: "E" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3979 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 18, 'TRANS': 478} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "T" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 733 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3979 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 18, 'TRANS': 478} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 733 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4432 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 7260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7260 Classifications: {'peptide': 924} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 32, 'TRANS': 891} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4432 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 7260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7260 Classifications: {'peptide': 924} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 32, 'TRANS': 891} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FRU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 78 Unusual residues: {'FRU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FRU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 78 Unusual residues: {'FRU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.78, per 1000 atoms: 0.21 Number of scatterers: 33058 At special positions: 0 Unit cell: (197.025, 161.88, 138.45, 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 128 16.00 Mg 4 11.99 O 6514 8.00 N 5520 7.00 C 20892 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: 3.01 Conformation dependent library (CDL) restraints added in 1.3 seconds 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7536 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 52 sheets defined 21.3% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'E' and resid 159 through 162 Processing helix chain 'E' and resid 254 through 261 Processing helix chain 'E' and resid 303 through 307 removed outlier: 3.759A pdb=" N ASP E 307 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 347 removed outlier: 3.952A pdb=" N TYR E 347 " --> pdb=" O ILE E 343 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 162 Processing helix chain 'M' and resid 254 through 261 Processing helix chain 'M' and resid 303 through 307 removed outlier: 3.759A pdb=" N ASP M 307 " --> pdb=" O ALA M 304 " (cutoff:3.500A) Processing helix chain 'M' and resid 340 through 347 removed outlier: 3.952A pdb=" N TYR M 347 " --> pdb=" O ILE M 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 removed outlier: 4.342A pdb=" N LEU B 5 " --> pdb=" O ASP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 23 removed outlier: 3.567A pdb=" N ALA B 20 " --> pdb=" O ASP B 17 " (cutoff:3.500A) Proline residue: B 22 - end of helix Processing helix chain 'B' and resid 24 through 39 removed outlier: 4.497A pdb=" N TRP B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 removed outlier: 3.911A 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 109 Processing helix chain 'B' and resid 118 through 141 Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.720A pdb=" N ASN B 158 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 185 removed outlier: 3.916A pdb=" N ASP B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 213 removed outlier: 3.939A pdb=" N TYR B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 removed outlier: 3.584A pdb=" N LEU B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.715A pdb=" N MET B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.680A pdb=" N GLU B 262 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 289 Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'B' and resid 340 through 344 Processing helix chain 'B' and resid 407 through 422 Processing helix chain 'B' and resid 425 through 443 removed outlier: 3.607A pdb=" N ALA B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 455 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 520 removed outlier: 3.563A pdb=" N TYR B 519 " --> pdb=" O CYS B 516 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 520 " --> pdb=" O SER B 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 520' Processing helix chain 'B' and resid 535 through 542 Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.912A 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: 4.269A 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 602 through 608 removed outlier: 5.686A pdb=" N ASN A 605 " --> pdb=" O THR A 602 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE A 606 " --> pdb=" O GLN A 603 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A 607 " --> pdb=" O GLU A 604 " (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 889 through 895 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 2 through 6 removed outlier: 4.342A pdb=" N LEU J 5 " --> pdb=" O ASP J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 23 removed outlier: 3.568A pdb=" N ALA J 20 " --> pdb=" O ASP J 17 " (cutoff:3.500A) Proline residue: J 22 - end of helix Processing helix chain 'J' and resid 24 through 39 removed outlier: 4.497A pdb=" N TRP J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA J 37 " --> pdb=" O TYR J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 55 removed outlier: 3.911A 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 109 Processing helix chain 'J' and resid 118 through 141 Processing helix chain 'J' and resid 153 through 160 removed outlier: 3.720A pdb=" N ASN J 158 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 185 removed outlier: 3.915A pdb=" N ASP J 177 " --> pdb=" O LYS J 173 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE J 178 " --> pdb=" O ILE J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 213 removed outlier: 3.939A pdb=" N TYR J 213 " --> pdb=" O LEU J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 237 removed outlier: 3.584A pdb=" N LEU J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 246 removed outlier: 3.714A pdb=" N MET J 242 " --> pdb=" O ASP J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 257 Processing helix chain 'J' and resid 258 through 262 removed outlier: 3.680A pdb=" N GLU J 262 " --> pdb=" O PRO J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 289 Processing helix chain 'J' and resid 293 through 297 Processing helix chain 'J' and resid 305 through 313 Processing helix chain 'J' and resid 340 through 344 Processing helix chain 'J' and resid 407 through 422 Processing helix chain 'J' and resid 425 through 443 removed outlier: 3.607A pdb=" N ALA J 429 " --> pdb=" O ARG J 425 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 455 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 520 removed outlier: 3.563A pdb=" N TYR J 519 " --> pdb=" O CYS J 516 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS J 520 " --> pdb=" O SER J 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 516 through 520' Processing helix chain 'J' and resid 535 through 542 Processing helix chain 'I' and resid 105 through 110 Processing helix chain 'I' and resid 111 through 113 No H-bonds generated for 'chain 'I' and resid 111 through 113' Processing helix chain 'I' and resid 116 through 121 Processing helix chain 'I' and resid 167 through 171 removed outlier: 3.912A 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: 4.268A 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 602 through 608 removed outlier: 5.685A pdb=" N ASN I 605 " --> pdb=" O THR I 602 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE I 606 " --> pdb=" O GLN I 603 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET I 607 " --> pdb=" O GLU I 604 " (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 889 through 895 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 'E' and resid 39 through 40 removed outlier: 3.672A pdb=" N ASP E 53 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 39 through 40 removed outlier: 7.365A pdb=" N ILE E 73 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU E 89 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLY E 75 " --> pdb=" O LEU E 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AA4, first strand: chain 'E' and resid 107 through 111 Processing sheet with id=AA5, first strand: chain 'E' and resid 168 through 175 removed outlier: 7.307A pdb=" N PHE E 168 " --> pdb=" O ARG E 188 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ARG E 188 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ASP E 170 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA E 186 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLY E 193 " --> pdb=" O MET E 213 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N MET E 213 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE E 195 " --> pdb=" O THR E 211 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N THR E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLU E 197 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 221 through 229 removed outlier: 6.691A pdb=" N ILE E 236 " --> pdb=" O PRO E 224 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL E 226 " --> pdb=" O TYR E 234 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR E 234 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS E 228 " --> pdb=" O TRP E 232 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 283 through 289 removed outlier: 6.058A pdb=" N ALA E 284 " --> pdb=" O TRP E 299 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP E 299 " --> pdb=" O ALA E 284 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ARG E 294 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 349 through 351 removed outlier: 4.107A pdb=" N VAL E 500 " --> pdb=" O GLN E 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 349 through 351 removed outlier: 4.107A pdb=" N VAL E 500 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL E 498 " --> pdb=" O SER E 389 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER E 389 " --> pdb=" O VAL E 498 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL E 500 " --> pdb=" O LYS E 387 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS E 387 " --> pdb=" O VAL E 500 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR E 502 " --> pdb=" O HIS E 385 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N HIS E 385 " --> pdb=" O THR E 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 355 through 358 removed outlier: 6.484A pdb=" N ILE E 378 " --> pdb=" O MET E 356 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LYS E 358 " --> pdb=" O SER E 376 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N SER E 376 " --> pdb=" O LYS E 358 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TRP E 484 " --> pdb=" O PHE E 379 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE E 401 " --> pdb=" O VAL E 419 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA E 426 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP E 440 " --> pdb=" O ALA E 426 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE E 428 " --> pdb=" O LEU E 438 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 25 through 26 removed outlier: 3.748A pdb=" N SER T 19 " --> pdb=" O ASN T 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU T 53 " --> pdb=" O ARG T 21 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 28 through 30 removed outlier: 6.122A pdb=" N ILE T 36 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LYS T 94 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL T 38 " --> pdb=" O LYS T 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 28 through 30 removed outlier: 6.122A pdb=" N ILE T 36 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LYS T 94 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL T 38 " --> pdb=" O LYS T 94 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU A 273 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY A 264 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 39 through 40 removed outlier: 3.672A pdb=" N ASP M 53 " --> pdb=" O ASP M 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 39 through 40 removed outlier: 7.365A pdb=" N ILE M 73 " --> pdb=" O GLU M 89 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU M 89 " --> pdb=" O ILE M 73 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLY M 75 " --> pdb=" O LEU M 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 102 through 103 Processing sheet with id=AB8, first strand: chain 'M' and resid 107 through 111 Processing sheet with id=AB9, first strand: chain 'M' and resid 168 through 175 removed outlier: 7.307A pdb=" N PHE M 168 " --> pdb=" O ARG M 188 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ARG M 188 " --> pdb=" O PHE M 168 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ASP M 170 " --> pdb=" O ALA M 186 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA M 186 " --> pdb=" O ASP M 170 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLY M 193 " --> pdb=" O MET M 213 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N MET M 213 " --> pdb=" O GLY M 193 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE M 195 " --> pdb=" O THR M 211 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR M 211 " --> pdb=" O ILE M 195 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLU M 197 " --> pdb=" O ALA M 209 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 221 through 229 removed outlier: 6.692A pdb=" N ILE M 236 " --> pdb=" O PRO M 224 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL M 226 " --> pdb=" O TYR M 234 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR M 234 " --> pdb=" O VAL M 226 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS M 228 " --> pdb=" O TRP M 232 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP M 232 " --> pdb=" O LYS M 228 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 283 through 289 removed outlier: 6.058A pdb=" N ALA M 284 " --> pdb=" O TRP M 299 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TRP M 299 " --> pdb=" O ALA M 284 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ARG M 294 " --> pdb=" O LEU M 327 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 349 through 351 removed outlier: 4.107A pdb=" N VAL M 500 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 349 through 351 removed outlier: 4.107A pdb=" N VAL M 500 " --> pdb=" O GLN M 351 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL M 498 " --> pdb=" O SER M 389 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER M 389 " --> pdb=" O VAL M 498 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL M 500 " --> pdb=" O LYS M 387 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS M 387 " --> pdb=" O VAL M 500 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR M 502 " --> pdb=" O HIS M 385 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N HIS M 385 " --> pdb=" O THR M 502 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 355 through 358 removed outlier: 6.484A pdb=" N ILE M 378 " --> pdb=" O MET M 356 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LYS M 358 " --> pdb=" O SER M 376 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N SER M 376 " --> pdb=" O LYS M 358 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TRP M 484 " --> pdb=" O PHE M 379 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE M 401 " --> pdb=" O VAL M 419 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA M 426 " --> pdb=" O ASP M 440 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP M 440 " --> pdb=" O ALA M 426 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE M 428 " --> pdb=" O LEU M 438 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 25 through 26 removed outlier: 3.748A pdb=" N SER G 19 " --> pdb=" O ASN G 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU G 53 " --> pdb=" O ARG G 21 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 28 through 30 removed outlier: 6.122A pdb=" N ILE G 36 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LYS G 94 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL G 38 " --> pdb=" O LYS G 94 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 28 through 30 removed outlier: 6.122A pdb=" N ILE G 36 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LYS G 94 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL G 38 " --> pdb=" O LYS G 94 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU I 273 " --> pdb=" O GLY I 264 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY I 264 " --> pdb=" O LEU I 273 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 14 through 15 removed outlier: 6.609A pdb=" N ILE A 638 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 267 through 271 removed outlier: 7.343A pdb=" N SER B 267 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ARG B 406 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP B 269 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 336 through 337 Processing sheet with id=AD3, first strand: chain 'B' and resid 345 through 346 Processing sheet with id=AD4, first strand: chain 'B' and resid 390 through 392 Processing sheet with id=AD5, first strand: chain 'A' and resid 101 through 104 removed outlier: 4.099A pdb=" N ILE A 179 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A 203 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE A 179 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 201 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL A 181 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A 199 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 156 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE A 202 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 158 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THR A 204 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 128 through 132 Processing sheet with id=AD7, first strand: chain 'A' and resid 211 through 224 removed outlier: 3.698A pdb=" N VAL A 304 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ARG A 421 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG A 457 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N THR A 591 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 7.340A 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: 6.660A pdb=" N ASP A 873 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU A 956 " --> pdb=" O ASP A 873 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 875 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE A 954 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE A 877 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE A 948 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 985 " --> pdb=" O PHE A 948 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS A 950 " --> pdb=" O LEU A 983 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU A 983 " --> pdb=" O LYS A 950 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ARG A 952 " --> pdb=" O ASN A 981 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AD9, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AE1, first strand: chain 'A' and resid 804 through 806 removed outlier: 6.811A pdb=" N GLN A 804 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.775A pdb=" N ARG A 834 " --> pdb=" O ASP A 810 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AE4, first strand: chain 'J' and resid 267 through 271 removed outlier: 7.342A pdb=" N SER J 267 " --> pdb=" O ARG J 406 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ARG J 406 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP J 269 " --> pdb=" O VAL J 404 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 336 through 337 Processing sheet with id=AE6, first strand: chain 'J' and resid 345 through 346 Processing sheet with id=AE7, first strand: chain 'J' and resid 390 through 392 Processing sheet with id=AE8, first strand: chain 'I' and resid 101 through 104 removed outlier: 4.101A pdb=" N ILE I 179 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR I 203 " --> pdb=" O GLU I 177 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE I 179 " --> pdb=" O ILE I 201 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE I 201 " --> pdb=" O ILE I 179 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL I 181 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL I 199 " --> pdb=" O VAL I 181 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU I 156 " --> pdb=" O ILE I 200 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE I 202 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE I 158 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THR I 204 " --> pdb=" O ILE I 158 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 128 through 132 Processing sheet with id=AF1, first strand: chain 'I' and resid 211 through 224 removed outlier: 3.698A pdb=" N VAL I 304 " --> pdb=" O LEU I 331 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ARG I 421 " --> pdb=" O ARG I 457 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG I 457 " --> pdb=" O ARG I 421 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N THR I 591 " --> pdb=" O GLY I 626 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY I 626 " --> pdb=" O THR I 591 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA I 740 " --> pdb=" O LEU I 776 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP I 873 " --> pdb=" O LEU I 956 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU I 956 " --> pdb=" O ASP I 873 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR I 875 " --> pdb=" O ILE I 954 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE I 954 " --> pdb=" O THR I 875 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE I 877 " --> pdb=" O ARG I 952 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE I 948 " --> pdb=" O ILE I 985 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE I 985 " --> pdb=" O PHE I 948 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS I 950 " --> pdb=" O LEU I 983 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU I 983 " --> pdb=" O LYS I 950 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ARG I 952 " --> pdb=" O ASN I 981 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 464 through 465 Processing sheet with id=AF3, first strand: chain 'I' and resid 638 through 640 removed outlier: 6.608A pdb=" N ILE I 638 " --> pdb=" O ASN I 676 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 719 through 722 Processing sheet with id=AF5, first strand: chain 'I' and resid 804 through 806 removed outlier: 6.811A pdb=" N GLN I 804 " --> pdb=" O ILE I 852 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 809 through 812 removed outlier: 4.775A pdb=" N ARG I 834 " --> pdb=" O ASP I 810 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 885 through 887 1454 hydrogen bonds defined for protein. 3909 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: 8.16 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10830 1.34 - 1.46: 6949 1.46 - 1.57: 15777 1.57 - 1.69: 66 1.69 - 1.81: 228 Bond restraints: 33850 Sorted by residual: 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 1.31e+02 bond pdb=" C2 FRU L 4 " pdb=" O5 FRU L 4 " ideal model delta sigma weight residual 1.412 1.641 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C2 FRU C 7 " pdb=" O5 FRU C 7 " ideal model delta sigma weight residual 1.412 1.638 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C2 FRU K 7 " pdb=" O5 FRU K 7 " ideal model delta sigma weight residual 1.412 1.637 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C2 FRU D 1 " pdb=" O5 FRU D 1 " ideal model delta sigma weight residual 1.412 1.637 -0.225 2.00e-02 2.50e+03 1.26e+02 ... (remaining 33845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 44971 1.73 - 3.46: 742 3.46 - 5.19: 133 5.19 - 6.91: 54 6.91 - 8.64: 14 Bond angle restraints: 45914 Sorted by residual: angle pdb=" C CYS J 298 " pdb=" N CYS J 299 " pdb=" CA CYS J 299 " ideal model delta sigma weight residual 121.54 130.18 -8.64 1.91e+00 2.74e-01 2.05e+01 angle pdb=" C CYS B 298 " pdb=" N CYS B 299 " pdb=" CA CYS B 299 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 angle pdb=" CA LYS A 318 " pdb=" CB LYS A 318 " pdb=" CG LYS A 318 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA LYS I 318 " pdb=" CB LYS I 318 " pdb=" CG LYS I 318 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" N CYS J 299 " pdb=" CA CYS J 299 " pdb=" C CYS J 299 " ideal model delta sigma weight residual 110.80 117.11 -6.31 2.13e+00 2.20e-01 8.77e+00 ... (remaining 45909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 18596 17.96 - 35.91: 922 35.91 - 53.87: 113 53.87 - 71.82: 22 71.82 - 89.78: 15 Dihedral angle restraints: 19668 sinusoidal: 7746 harmonic: 11922 Sorted by residual: dihedral pdb=" CB CYS B 387 " pdb=" SG CYS B 387 " pdb=" SG CYS B 389 " pdb=" CB CYS B 389 " ideal model delta sinusoidal sigma weight residual -86.00 -149.13 63.13 1 1.00e+01 1.00e-02 5.26e+01 dihedral pdb=" CB CYS J 387 " pdb=" SG CYS J 387 " pdb=" SG CYS J 389 " pdb=" CB CYS J 389 " ideal model delta sinusoidal sigma weight residual -86.00 -149.12 63.12 1 1.00e+01 1.00e-02 5.26e+01 dihedral pdb=" CA CYS J 389 " pdb=" C CYS J 389 " pdb=" N LEU J 390 " pdb=" CA LEU J 390 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 19665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2754 0.031 - 0.063: 1336 0.063 - 0.094: 458 0.094 - 0.125: 255 0.125 - 0.157: 45 Chirality restraints: 4848 Sorted by residual: 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 2.76 -0.16 2.00e-02 2.50e+03 6.14e+01 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 2.75 -0.15 2.00e-02 2.50e+03 5.98e+01 chirality pdb=" C2 FRU D 4 " pdb=" O6 FRU D 3 " pdb=" C1 FRU D 4 " pdb=" O5 FRU D 4 " both_signs ideal model delta sigma weight residual False 2.60 2.68 -0.08 2.00e-02 2.50e+03 1.48e+01 ... (remaining 4845 not shown) Planarity restraints: 5976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL T 40 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO T 41 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO T 41 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO T 41 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 40 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO G 41 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO G 41 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 41 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 127 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO E 128 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 128 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 128 " -0.018 5.00e-02 4.00e+02 ... (remaining 5973 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 351 2.56 - 3.15: 26912 3.15 - 3.73: 51668 3.73 - 4.32: 76225 4.32 - 4.90: 129184 Nonbonded interactions: 284340 Sorted by model distance: nonbonded pdb=" OD1 ASN J 401 " pdb="MG MG J 601 " model vdw 1.978 2.170 nonbonded pdb=" OD1 ASN B 401 " pdb="MG MG B 601 " model vdw 1.978 2.170 nonbonded pdb=" OD2 ASP I 848 " pdb="MG MG I1101 " model vdw 2.057 2.170 nonbonded pdb=" OD2 ASP A 848 " pdb="MG MG A1101 " model vdw 2.058 2.170 nonbonded pdb=" ND2 ASN I 664 " pdb="MG MG J 601 " model vdw 2.059 2.250 ... (remaining 284335 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: 0.07 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'T' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.740 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 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 : 0.010 0.229 33870 Z= 0.511 Angle : 0.628 8.644 45972 Z= 0.316 Chirality : 0.045 0.157 4848 Planarity : 0.003 0.039 5976 Dihedral : 10.928 89.780 12126 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.44 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.13), residues: 4118 helix: 1.59 (0.20), residues: 732 sheet: 0.42 (0.15), residues: 1256 loop : -0.37 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 367 TYR 0.017 0.001 TYR I 225 PHE 0.018 0.001 PHE A1016 TRP 0.011 0.001 TRP I 851 HIS 0.008 0.001 HIS M 71 Details of bonding type rmsd/Z covalent geometry : bond 0.01032 / 0.50 (33850) covalent geometry : angle 0.61590 / 0.31 (45914) SS BOND : bond 0.00762 / 0.52 ( 2) SS BOND : angle 1.66769 / 1.01 ( 4) hydrogen bonds : bond 0.10397 / 6.75 ( 1420) hydrogen bonds : angle 5.55736 / 3.90 ( 3909) glycosidic custom : bond 0.04512 / 3.12 ( 2) glycosidic custom : angle 3.58794 / 2.24 ( 6) link_ALPHA2-6 : bond 0.08697 / 5.39 ( 16) link_ALPHA2-6 : angle 3.56868 / 2.36 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: E 276 MET cc_start: 0.8066 (mmm) cc_final: 0.7750 (mmt) REVERT: G 30 ASP cc_start: 0.8229 (t0) cc_final: 0.7996 (t0) REVERT: B 465 LEU cc_start: 0.9199 (mt) cc_final: 0.8994 (mm) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2017 time to fit residues: 66.4208 Evaluate side-chains 151 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 HIS ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 GLN B 43 ASN B 336 ASN A 153 ASN A 372 GLN ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN I 243 GLN I 247 ASN ** I 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 632 ASN I 744 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.069705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.051681 restraints weight = 85183.243| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.29 r_work: 0.2663 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 33870 Z= 0.245 Angle : 0.583 9.012 45972 Z= 0.307 Chirality : 0.045 0.165 4848 Planarity : 0.004 0.042 5976 Dihedral : 4.302 26.102 4558 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.03 % Favored : 95.77 % Rotamer: Outliers : 0.43 % Allowed : 3.65 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.13), residues: 4118 helix: 1.43 (0.20), residues: 722 sheet: 0.38 (0.15), residues: 1258 loop : -0.38 (0.14), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 21 TYR 0.019 0.002 TYR A 225 PHE 0.016 0.001 PHE B 342 TRP 0.013 0.001 TRP J 36 HIS 0.005 0.001 HIS J 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (33850) covalent geometry : angle 0.57351 / 0.30 (45914) SS BOND : bond 0.04473 / 3.09 ( 2) SS BOND : angle 0.65465 / 0.53 ( 4) hydrogen bonds : bond 0.03991 / 2.57 ( 1420) hydrogen bonds : angle 5.00781 / 3.49 ( 3909) glycosidic custom : bond 0.01204 / 0.83 ( 2) glycosidic custom : angle 2.69361 / 1.72 ( 6) link_ALPHA2-6 : bond 0.01500 / 1.05 ( 16) link_ALPHA2-6 : angle 3.13464 / 2.03 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 216 MET cc_start: 0.6768 (mmm) cc_final: 0.6411 (mmm) REVERT: E 276 MET cc_start: 0.8196 (mmm) cc_final: 0.7741 (mmt) REVERT: T 12 ASP cc_start: 0.8436 (m-30) cc_final: 0.7997 (p0) REVERT: M 356 MET cc_start: 0.9140 (mmm) cc_final: 0.8852 (mmm) REVERT: G 30 ASP cc_start: 0.8541 (t0) cc_final: 0.8170 (t0) REVERT: G 48 ARG cc_start: 0.8485 (mmm160) cc_final: 0.8148 (mmm160) REVERT: G 49 MET cc_start: 0.8106 (mpp) cc_final: 0.7330 (mpp) REVERT: B 7 ARG cc_start: 0.7967 (ttm170) cc_final: 0.7656 (mtp180) REVERT: I 777 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8493 (tt0) outliers start: 15 outliers final: 7 residues processed: 171 average time/residue: 0.2148 time to fit residues: 60.3738 Evaluate side-chains 156 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 509 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 113 optimal weight: 10.0000 chunk 381 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 402 optimal weight: 0.6980 chunk 374 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 319 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 300 optimal weight: 0.7980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 71 HIS E 133 ASN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN J 43 ASN I 309 ASN ** I 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 632 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.070287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.052400 restraints weight = 84440.874| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.29 r_work: 0.2675 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33870 Z= 0.160 Angle : 0.524 9.135 45972 Z= 0.277 Chirality : 0.044 0.174 4848 Planarity : 0.003 0.039 5976 Dihedral : 4.168 32.204 4558 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.62 % Favored : 96.19 % Rotamer: Outliers : 0.58 % Allowed : 5.15 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.13), residues: 4118 helix: 1.48 (0.20), residues: 722 sheet: 0.43 (0.14), residues: 1258 loop : -0.39 (0.14), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 95 TYR 0.013 0.001 TYR A 225 PHE 0.011 0.001 PHE B 342 TRP 0.011 0.001 TRP B 91 HIS 0.003 0.001 HIS J 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (33850) covalent geometry : angle 0.51430 / 0.27 (45914) SS BOND : bond 0.00958 / 0.66 ( 2) SS BOND : angle 5.52457 / 3.52 ( 4) hydrogen bonds : bond 0.03486 / 2.25 ( 1420) hydrogen bonds : angle 4.75840 / 3.31 ( 3909) glycosidic custom : bond 0.01383 / 0.96 ( 2) glycosidic custom : angle 2.17775 / 1.47 ( 6) link_ALPHA2-6 : bond 0.01317 / 0.88 ( 16) link_ALPHA2-6 : angle 2.59738 / 1.71 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 216 MET cc_start: 0.6882 (mmm) cc_final: 0.6462 (mmm) REVERT: T 12 ASP cc_start: 0.8354 (m-30) cc_final: 0.7989 (p0) REVERT: T 49 MET cc_start: 0.8273 (mpp) cc_final: 0.7552 (mpp) REVERT: M 183 MET cc_start: 0.9241 (ttp) cc_final: 0.8985 (ttm) REVERT: M 356 MET cc_start: 0.9154 (mmm) cc_final: 0.8818 (mmm) REVERT: G 19 SER cc_start: 0.9123 (m) cc_final: 0.8922 (m) REVERT: G 30 ASP cc_start: 0.8567 (t0) cc_final: 0.8218 (t0) REVERT: G 49 MET cc_start: 0.8275 (mpp) cc_final: 0.7479 (mpp) REVERT: A 108 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8215 (pm20) REVERT: I 108 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8386 (pm20) REVERT: I 777 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8482 (tt0) REVERT: I 968 MET cc_start: 0.8434 (ttm) cc_final: 0.8202 (ttm) outliers start: 20 outliers final: 12 residues processed: 173 average time/residue: 0.2176 time to fit residues: 62.5704 Evaluate side-chains 163 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 84 ASP Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 213 optimal weight: 0.9990 chunk 341 optimal weight: 1.9990 chunk 345 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 340 optimal weight: 5.9990 chunk 387 optimal weight: 0.9990 chunk 277 optimal weight: 0.0670 chunk 82 optimal weight: 9.9990 chunk 289 optimal weight: 7.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 71 HIS ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 HIS A 309 ASN ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN I 468 GLN ** I 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.070252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.052282 restraints weight = 84043.267| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.34 r_work: 0.2675 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33870 Z= 0.142 Angle : 0.508 14.386 45972 Z= 0.267 Chirality : 0.043 0.195 4848 Planarity : 0.003 0.037 5976 Dihedral : 4.073 24.047 4558 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.74 % Favored : 96.09 % Rotamer: Outliers : 0.72 % Allowed : 6.53 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.13), residues: 4118 helix: 1.51 (0.20), residues: 722 sheet: 0.45 (0.15), residues: 1262 loop : -0.36 (0.14), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 10 TYR 0.017 0.001 TYR G 42 PHE 0.011 0.001 PHE B 342 TRP 0.011 0.001 TRP B 91 HIS 0.003 0.001 HIS M 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (33850) covalent geometry : angle 0.49986 / 0.26 (45914) SS BOND : bond 0.00275 / 0.19 ( 2) SS BOND : angle 3.41748 / 2.24 ( 4) hydrogen bonds : bond 0.03281 / 2.12 ( 1420) hydrogen bonds : angle 4.65376 / 3.23 ( 3909) glycosidic custom : bond 0.01123 / 0.78 ( 2) glycosidic custom : angle 2.29541 / 1.55 ( 6) link_ALPHA2-6 : bond 0.01172 / 0.77 ( 16) link_ALPHA2-6 : angle 2.57609 / 1.72 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 49 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7549 (mpp) REVERT: M 183 MET cc_start: 0.9259 (ttp) cc_final: 0.8995 (ttm) REVERT: M 356 MET cc_start: 0.9165 (mmm) cc_final: 0.8806 (mmm) REVERT: G 30 ASP cc_start: 0.8581 (t0) cc_final: 0.8221 (t0) REVERT: G 48 ARG cc_start: 0.8847 (mmm-85) cc_final: 0.8411 (mmm160) REVERT: G 49 MET cc_start: 0.8196 (mpp) cc_final: 0.7578 (mpp) REVERT: G 56 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7400 (mt) REVERT: A 108 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8233 (pm20) REVERT: J 111 MET cc_start: 0.9027 (ttm) cc_final: 0.8795 (ttm) REVERT: J 288 MET cc_start: 0.9385 (mmt) cc_final: 0.9085 (mmt) REVERT: I 108 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8283 (pm20) REVERT: I 968 MET cc_start: 0.8491 (ttm) cc_final: 0.8283 (ttm) outliers start: 25 outliers final: 16 residues processed: 172 average time/residue: 0.1999 time to fit residues: 57.5905 Evaluate side-chains 172 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 977 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 144 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 398 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 400 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 322 optimal weight: 1.9990 chunk 323 optimal weight: 0.6980 chunk 276 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 71 HIS ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN ** I 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.067265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.049368 restraints weight = 85067.059| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.31 r_work: 0.2601 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 33870 Z= 0.279 Angle : 0.593 11.352 45972 Z= 0.312 Chirality : 0.046 0.191 4848 Planarity : 0.004 0.055 5976 Dihedral : 4.443 24.639 4558 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.32 % Favored : 95.51 % Rotamer: Outliers : 1.01 % Allowed : 7.07 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.13), residues: 4118 helix: 1.35 (0.20), residues: 720 sheet: 0.30 (0.14), residues: 1262 loop : -0.45 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 515 TYR 0.024 0.002 TYR J 203 PHE 0.017 0.002 PHE B 342 TRP 0.017 0.001 TRP J 36 HIS 0.005 0.001 HIS M 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.28 (33850) covalent geometry : angle 0.58671 / 0.31 (45914) SS BOND : bond 0.00092 / 0.06 ( 2) SS BOND : angle 0.96776 / 0.58 ( 4) hydrogen bonds : bond 0.04081 / 2.62 ( 1420) hydrogen bonds : angle 5.00697 / 3.48 ( 3909) glycosidic custom : bond 0.00912 / 0.63 ( 2) glycosidic custom : angle 2.24995 / 1.52 ( 6) link_ALPHA2-6 : bond 0.01004 / 0.66 ( 16) link_ALPHA2-6 : angle 2.63165 / 1.75 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.407 Fit side-chains REVERT: E 276 MET cc_start: 0.8215 (mmm) cc_final: 0.7944 (mmt) REVERT: T 49 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7484 (mpp) REVERT: M 276 MET cc_start: 0.8046 (mmm) cc_final: 0.7369 (mmt) REVERT: G 30 ASP cc_start: 0.8622 (t0) cc_final: 0.8312 (t0) REVERT: G 49 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7514 (mpp) REVERT: G 56 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7726 (mt) REVERT: B 7 ARG cc_start: 0.7980 (ttm170) cc_final: 0.7736 (mtp180) REVERT: A 108 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8225 (pm20) REVERT: I 108 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: I 968 MET cc_start: 0.8374 (ttm) cc_final: 0.8017 (ttm) outliers start: 35 outliers final: 22 residues processed: 166 average time/residue: 0.2080 time to fit residues: 57.5840 Evaluate side-chains 168 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 134 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 368 optimal weight: 0.3980 chunk 144 optimal weight: 3.9990 chunk 393 optimal weight: 0.7980 chunk 407 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 ASN I 151 ASN ** I 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.070088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.052532 restraints weight = 83640.324| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.36 r_work: 0.2684 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33870 Z= 0.115 Angle : 0.512 11.515 45972 Z= 0.269 Chirality : 0.043 0.203 4848 Planarity : 0.003 0.039 5976 Dihedral : 4.194 32.075 4558 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.06 % Favored : 96.79 % Rotamer: Outliers : 0.92 % Allowed : 7.48 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.13), residues: 4118 helix: 1.50 (0.20), residues: 708 sheet: 0.36 (0.15), residues: 1244 loop : -0.39 (0.14), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 294 TYR 0.016 0.001 TYR J 203 PHE 0.013 0.001 PHE J 301 TRP 0.014 0.001 TRP I 486 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (33850) covalent geometry : angle 0.50172 / 0.27 (45914) SS BOND : bond 0.00689 / 0.48 ( 2) SS BOND : angle 6.42933 / 4.19 ( 4) hydrogen bonds : bond 0.03221 / 2.08 ( 1420) hydrogen bonds : angle 4.68296 / 3.25 ( 3909) glycosidic custom : bond 0.01243 / 0.86 ( 2) glycosidic custom : angle 2.27565 / 1.57 ( 6) link_ALPHA2-6 : bond 0.01146 / 0.72 ( 16) link_ALPHA2-6 : angle 2.48960 / 1.70 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 244 MET cc_start: 0.8635 (tpp) cc_final: 0.8382 (tpp) REVERT: T 49 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7332 (mpp) REVERT: T 56 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7089 (mt) REVERT: M 244 MET cc_start: 0.8880 (tpp) cc_final: 0.8541 (tpp) REVERT: M 356 MET cc_start: 0.9129 (mmm) cc_final: 0.8835 (mmm) REVERT: G 19 SER cc_start: 0.8950 (m) cc_final: 0.8519 (p) REVERT: G 30 ASP cc_start: 0.8585 (t0) cc_final: 0.8266 (t0) REVERT: G 48 ARG cc_start: 0.8916 (mmm-85) cc_final: 0.8480 (mmm160) REVERT: G 49 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7300 (mpp) REVERT: G 56 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7279 (mt) REVERT: A 108 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8365 (pm20) REVERT: I 108 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8428 (pm20) REVERT: I 777 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8364 (tm-30) outliers start: 32 outliers final: 17 residues processed: 175 average time/residue: 0.2122 time to fit residues: 62.7517 Evaluate side-chains 167 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 977 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 138 optimal weight: 0.3980 chunk 348 optimal weight: 10.0000 chunk 312 optimal weight: 4.9990 chunk 234 optimal weight: 7.9990 chunk 405 optimal weight: 10.0000 chunk 274 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 318 optimal weight: 0.3980 chunk 80 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN ** I 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.068558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.050900 restraints weight = 84791.619| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.34 r_work: 0.2639 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 33870 Z= 0.222 Angle : 0.549 10.495 45972 Z= 0.288 Chirality : 0.045 0.211 4848 Planarity : 0.003 0.044 5976 Dihedral : 4.265 31.812 4558 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.23 % Favored : 95.63 % Rotamer: Outliers : 1.09 % Allowed : 7.79 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.13), residues: 4118 helix: 1.42 (0.20), residues: 720 sheet: 0.34 (0.15), residues: 1256 loop : -0.46 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 515 TYR 0.019 0.001 TYR J 203 PHE 0.014 0.001 PHE B 342 TRP 0.011 0.001 TRP B 36 HIS 0.004 0.001 HIS J 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (33850) covalent geometry : angle 0.54040 / 0.29 (45914) SS BOND : bond 0.01001 / 0.69 ( 2) SS BOND : angle 4.84527 / 3.17 ( 4) hydrogen bonds : bond 0.03645 / 2.34 ( 1420) hydrogen bonds : angle 4.79508 / 3.33 ( 3909) glycosidic custom : bond 0.01017 / 0.70 ( 2) glycosidic custom : angle 2.26267 / 1.53 ( 6) link_ALPHA2-6 : bond 0.01015 / 0.66 ( 16) link_ALPHA2-6 : angle 2.59799 / 1.75 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 244 MET cc_start: 0.8812 (tpp) cc_final: 0.8485 (tpp) REVERT: E 276 MET cc_start: 0.7962 (mmm) cc_final: 0.7180 (mmt) REVERT: T 49 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7322 (mpp) REVERT: T 56 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7078 (mt) REVERT: M 156 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8528 (tt) REVERT: M 276 MET cc_start: 0.7906 (mmm) cc_final: 0.6959 (mmt) REVERT: M 356 MET cc_start: 0.9101 (mmm) cc_final: 0.8800 (mmm) REVERT: G 30 ASP cc_start: 0.8583 (t0) cc_final: 0.8196 (t0) REVERT: G 46 ILE cc_start: 0.8693 (pt) cc_final: 0.8280 (pt) REVERT: G 48 ARG cc_start: 0.8904 (mmm-85) cc_final: 0.8526 (mmm160) REVERT: G 49 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7289 (mpp) REVERT: G 56 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7458 (mt) REVERT: A 108 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8289 (pm20) REVERT: A 506 MET cc_start: 0.8894 (tmm) cc_final: 0.8687 (tmm) REVERT: I 108 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: I 777 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8450 (tt0) REVERT: I 968 MET cc_start: 0.8431 (ttm) cc_final: 0.8062 (ttm) outliers start: 38 outliers final: 23 residues processed: 167 average time/residue: 0.2114 time to fit residues: 59.5867 Evaluate side-chains 172 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 427 MET Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 977 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 409 optimal weight: 1.9990 chunk 314 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 395 optimal weight: 0.9980 chunk 53 optimal weight: 0.0870 chunk 208 optimal weight: 0.9990 chunk 362 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN I 151 ASN ** I 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.070633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.053259 restraints weight = 83654.795| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.35 r_work: 0.2694 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33870 Z= 0.100 Angle : 0.492 12.348 45972 Z= 0.258 Chirality : 0.042 0.199 4848 Planarity : 0.003 0.038 5976 Dihedral : 4.033 27.011 4558 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.23 % Favored : 96.62 % Rotamer: Outliers : 0.83 % Allowed : 8.19 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 4118 helix: 1.41 (0.20), residues: 732 sheet: 0.40 (0.15), residues: 1244 loop : -0.37 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 95 TYR 0.021 0.001 TYR T 42 PHE 0.011 0.001 PHE J 301 TRP 0.015 0.001 TRP I 486 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (33850) covalent geometry : angle 0.48424 / 0.26 (45914) SS BOND : bond 0.00752 / 0.52 ( 2) SS BOND : angle 3.55756 / 2.49 ( 4) hydrogen bonds : bond 0.03016 / 1.94 ( 1420) hydrogen bonds : angle 4.53554 / 3.16 ( 3909) glycosidic custom : bond 0.01232 / 0.85 ( 2) glycosidic custom : angle 2.25131 / 1.56 ( 6) link_ALPHA2-6 : bond 0.01125 / 0.71 ( 16) link_ALPHA2-6 : angle 2.48330 / 1.70 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 244 MET cc_start: 0.8620 (tpp) cc_final: 0.8185 (tpp) REVERT: E 276 MET cc_start: 0.7840 (mmm) cc_final: 0.7230 (mmt) REVERT: T 19 SER cc_start: 0.8859 (m) cc_final: 0.8410 (p) REVERT: T 49 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7338 (mpp) REVERT: T 56 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7335 (mt) REVERT: M 229 MET cc_start: 0.8686 (tpp) cc_final: 0.8235 (ttm) REVERT: M 244 MET cc_start: 0.8769 (tpp) cc_final: 0.8366 (tpp) REVERT: M 276 MET cc_start: 0.7864 (mmm) cc_final: 0.6780 (mmt) REVERT: M 356 MET cc_start: 0.9122 (mmm) cc_final: 0.8810 (mmm) REVERT: G 19 SER cc_start: 0.8976 (m) cc_final: 0.8518 (p) REVERT: G 30 ASP cc_start: 0.8614 (t0) cc_final: 0.8334 (t0) REVERT: G 48 ARG cc_start: 0.8861 (mmm-85) cc_final: 0.8391 (mmm160) REVERT: G 49 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7397 (mpp) REVERT: G 56 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7180 (mt) REVERT: A 108 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8324 (pm20) REVERT: I 108 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: I 777 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8381 (tm-30) outliers start: 29 outliers final: 20 residues processed: 174 average time/residue: 0.2185 time to fit residues: 63.7733 Evaluate side-chains 174 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 427 MET Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 977 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 112 optimal weight: 20.0000 chunk 231 optimal weight: 10.0000 chunk 204 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 301 optimal weight: 1.9990 chunk 240 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN ** I 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.066869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.049200 restraints weight = 85334.872| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 2.33 r_work: 0.2595 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 33870 Z= 0.370 Angle : 0.645 12.192 45972 Z= 0.337 Chirality : 0.048 0.249 4848 Planarity : 0.004 0.050 5976 Dihedral : 4.522 27.812 4558 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.29 % Rotamer: Outliers : 0.98 % Allowed : 8.17 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.13), residues: 4118 helix: 1.27 (0.20), residues: 716 sheet: 0.24 (0.14), residues: 1256 loop : -0.57 (0.14), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 515 TYR 0.023 0.002 TYR B 203 PHE 0.018 0.002 PHE J 342 TRP 0.016 0.002 TRP B 36 HIS 0.006 0.001 HIS M 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00849 / 0.37 (33850) covalent geometry : angle 0.63783 / 0.34 (45914) SS BOND : bond 0.00843 / 0.58 ( 2) SS BOND : angle 3.97754 / 2.44 ( 4) hydrogen bonds : bond 0.04277 / 2.75 ( 1420) hydrogen bonds : angle 5.05700 / 3.52 ( 3909) glycosidic custom : bond 0.00810 / 0.56 ( 2) glycosidic custom : angle 2.29297 / 1.56 ( 6) link_ALPHA2-6 : bond 0.00887 / 0.59 ( 16) link_ALPHA2-6 : angle 2.80147 / 1.87 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 216 MET cc_start: 0.7291 (mmm) cc_final: 0.6999 (mmm) REVERT: E 244 MET cc_start: 0.8941 (tpp) cc_final: 0.8491 (tpp) REVERT: E 276 MET cc_start: 0.8021 (mmm) cc_final: 0.7511 (mmt) REVERT: T 49 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7348 (mpp) REVERT: T 53 GLU cc_start: 0.8434 (pp20) cc_final: 0.8082 (pp20) REVERT: T 56 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7093 (mt) REVERT: M 229 MET cc_start: 0.8736 (tpp) cc_final: 0.8235 (ttm) REVERT: M 356 MET cc_start: 0.9078 (mmm) cc_final: 0.8757 (mmm) REVERT: G 30 ASP cc_start: 0.8733 (t0) cc_final: 0.8324 (t0) REVERT: G 49 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7315 (mpp) REVERT: G 56 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7318 (mt) REVERT: A 108 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: I 108 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8333 (pm20) REVERT: I 777 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8487 (tt0) REVERT: I 968 MET cc_start: 0.8274 (ttm) cc_final: 0.8046 (ttm) outliers start: 34 outliers final: 25 residues processed: 164 average time/residue: 0.2058 time to fit residues: 56.6897 Evaluate side-chains 174 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 495 VAL Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 427 MET Chi-restraints excluded: chain I residue 453 ASN Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 977 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 190 optimal weight: 0.0770 chunk 23 optimal weight: 0.5980 chunk 358 optimal weight: 0.6980 chunk 275 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 344 optimal weight: 0.8980 chunk 394 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 71 HIS ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN ** I 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.069982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.052615 restraints weight = 84219.139| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.34 r_work: 0.2677 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33870 Z= 0.106 Angle : 0.512 11.617 45972 Z= 0.269 Chirality : 0.043 0.239 4848 Planarity : 0.003 0.040 5976 Dihedral : 4.162 23.125 4558 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.13 % Favored : 96.77 % Rotamer: Outliers : 0.75 % Allowed : 8.37 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.13), residues: 4118 helix: 1.28 (0.20), residues: 732 sheet: 0.31 (0.15), residues: 1248 loop : -0.43 (0.14), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 10 TYR 0.019 0.001 TYR T 42 PHE 0.011 0.001 PHE B 301 TRP 0.018 0.001 TRP I 486 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (33850) covalent geometry : angle 0.50425 / 0.27 (45914) SS BOND : bond 0.00555 / 0.38 ( 2) SS BOND : angle 3.42423 / 2.35 ( 4) hydrogen bonds : bond 0.03157 / 2.03 ( 1420) hydrogen bonds : angle 4.65009 / 3.24 ( 3909) glycosidic custom : bond 0.01327 / 0.92 ( 2) glycosidic custom : angle 2.30577 / 1.63 ( 6) link_ALPHA2-6 : bond 0.01139 / 0.70 ( 16) link_ALPHA2-6 : angle 2.50276 / 1.73 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 215 MET cc_start: 0.8346 (mtt) cc_final: 0.7643 (mtt) REVERT: E 216 MET cc_start: 0.7061 (mmm) cc_final: 0.6752 (mmm) REVERT: E 276 MET cc_start: 0.7837 (mmm) cc_final: 0.7289 (mmt) REVERT: T 19 SER cc_start: 0.8891 (m) cc_final: 0.8447 (p) REVERT: T 49 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7386 (mpp) REVERT: T 56 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7323 (mt) REVERT: M 229 MET cc_start: 0.8746 (tpp) cc_final: 0.8270 (ttm) REVERT: M 244 MET cc_start: 0.8778 (tpp) cc_final: 0.8389 (tpp) REVERT: M 276 MET cc_start: 0.7693 (mmm) cc_final: 0.6736 (mmt) REVERT: M 356 MET cc_start: 0.9106 (mmm) cc_final: 0.8793 (mmm) REVERT: G 19 SER cc_start: 0.8972 (m) cc_final: 0.8528 (p) REVERT: G 30 ASP cc_start: 0.8606 (t0) cc_final: 0.8386 (t0) REVERT: G 48 ARG cc_start: 0.8880 (mmm-85) cc_final: 0.8435 (mmm160) REVERT: G 49 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7276 (mpp) REVERT: G 56 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7150 (mt) REVERT: A 108 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: I 108 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: I 777 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8422 (tm-30) REVERT: I 968 MET cc_start: 0.8205 (ttm) cc_final: 0.7983 (ttm) outliers start: 26 outliers final: 19 residues processed: 167 average time/residue: 0.2061 time to fit residues: 57.8609 Evaluate side-chains 173 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 427 MET Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 977 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 222 optimal weight: 5.9990 chunk 325 optimal weight: 4.9990 chunk 281 optimal weight: 3.9990 chunk 390 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 369 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN ** I 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.067716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.049954 restraints weight = 85057.884| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.37 r_work: 0.2613 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 33870 Z= 0.288 Angle : 0.588 11.805 45972 Z= 0.307 Chirality : 0.046 0.235 4848 Planarity : 0.004 0.053 5976 Dihedral : 4.343 27.058 4558 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 0.95 % Allowed : 8.19 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.13), residues: 4118 helix: 1.22 (0.20), residues: 732 sheet: 0.27 (0.15), residues: 1256 loop : -0.56 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 515 TYR 0.021 0.002 TYR T 42 PHE 0.016 0.001 PHE J 342 TRP 0.013 0.001 TRP B 36 HIS 0.005 0.001 HIS E 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.29 (33850) covalent geometry : angle 0.58058 / 0.31 (45914) SS BOND : bond 0.00745 / 0.51 ( 2) SS BOND : angle 3.57461 / 2.21 ( 4) hydrogen bonds : bond 0.03832 / 2.46 ( 1420) hydrogen bonds : angle 4.87767 / 3.40 ( 3909) glycosidic custom : bond 0.00912 / 0.63 ( 2) glycosidic custom : angle 2.20211 / 1.50 ( 6) link_ALPHA2-6 : bond 0.00906 / 0.59 ( 16) link_ALPHA2-6 : angle 2.71928 / 1.83 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7406.90 seconds wall clock time: 128 minutes 28.72 seconds (7708.72 seconds total)