Starting phenix.real_space_refine on Fri May 30 04:01:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aa0_15289/05_2025/8aa0_15289.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aa0_15289/05_2025/8aa0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8aa0_15289/05_2025/8aa0_15289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aa0_15289/05_2025/8aa0_15289.map" model { file = "/net/cci-nas-00/data/ceres_data/8aa0_15289/05_2025/8aa0_15289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aa0_15289/05_2025/8aa0_15289.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 4 5.21 5 S 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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 dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 78 Unusual residues: {'FRU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FRU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 78 Unusual residues: {'FRU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.71, per 1000 atoms: 0.51 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: 8.74 Conformation dependent library (CDL) restraints added in 4.5 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: 4.37 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: 14.25 Time building geometry restraints manager: 9.92 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: 18756 17.96 - 35.91: 1042 35.91 - 53.87: 201 53.87 - 71.82: 106 71.82 - 89.78: 19 Dihedral angle restraints: 20124 sinusoidal: 8202 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 20121 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: 0.16 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'T' } 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.430 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 71.590 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.170 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 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 : 12.833 89.780 12582 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (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 TRP 0.011 0.001 TRP I 851 HIS 0.008 0.001 HIS M 71 PHE 0.018 0.001 PHE A1016 TYR 0.017 0.001 TYR I 225 ARG 0.004 0.001 ARG I 367 Details of bonding type rmsd link_ALPHA2-6 : bond 0.08697 ( 16) link_ALPHA2-6 : angle 3.56868 ( 48) hydrogen bonds : bond 0.10397 ( 1420) hydrogen bonds : angle 5.55736 ( 3909) SS BOND : bond 0.00762 ( 2) SS BOND : angle 1.66769 ( 4) glycosidic custom : bond 0.04512 ( 2) glycosidic custom : angle 3.58794 ( 6) covalent geometry : bond 0.01032 (33850) covalent geometry : angle 0.61590 (45914) *********************** 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 : 3.758 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: 0.4489 time to fit residues: 148.3134 Evaluate side-chains 152 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 346 optimal weight: 0.9980 chunk 310 optimal weight: 1.9990 chunk 172 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 209 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 chunk 321 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 372 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 HIS ** 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 468 GLN A 632 ASN I 243 GLN I 247 ASN I 632 ASN I 744 GLN I 816 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.072778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.054731 restraints weight = 83914.623| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.34 r_work: 0.2743 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 33870 Z= 0.115 Angle : 0.524 8.111 45972 Z= 0.275 Chirality : 0.043 0.164 4848 Planarity : 0.003 0.039 5976 Dihedral : 7.927 53.671 5014 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.50 % Favored : 96.31 % Rotamer: Outliers : 0.43 % Allowed : 3.02 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.13), residues: 4118 helix: 1.64 (0.20), residues: 722 sheet: 0.62 (0.15), residues: 1218 loop : -0.35 (0.14), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 91 HIS 0.004 0.001 HIS M 71 PHE 0.010 0.001 PHE J 301 TYR 0.014 0.001 TYR I 225 ARG 0.004 0.000 ARG G 21 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01365 ( 16) link_ALPHA2-6 : angle 3.05038 ( 48) hydrogen bonds : bond 0.03417 ( 1420) hydrogen bonds : angle 4.78912 ( 3909) SS BOND : bond 0.01496 ( 2) SS BOND : angle 0.23822 ( 4) glycosidic custom : bond 0.00571 ( 2) glycosidic custom : angle 2.96133 ( 6) covalent geometry : bond 0.00243 (33850) covalent geometry : angle 0.51375 (45914) *********************** 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 191 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 3.523 Fit side-chains revert: symmetry clash REVERT: E 215 MET cc_start: 0.7837 (mtt) cc_final: 0.7439 (mtt) REVERT: E 216 MET cc_start: 0.6718 (mmm) cc_final: 0.6330 (mmm) REVERT: E 276 MET cc_start: 0.8127 (mmm) cc_final: 0.7656 (mmt) REVERT: T 10 ARG cc_start: 0.9027 (ptp90) cc_final: 0.8778 (ptp90) REVERT: M 44 MET cc_start: 0.8852 (mtt) cc_final: 0.8540 (mtt) REVERT: M 356 MET cc_start: 0.9131 (mmm) cc_final: 0.8838 (mmm) REVERT: G 30 ASP cc_start: 0.8438 (t0) cc_final: 0.8073 (t0) REVERT: G 48 ARG cc_start: 0.8348 (mmm160) cc_final: 0.7971 (mmm160) outliers start: 15 outliers final: 8 residues processed: 182 average time/residue: 0.4661 time to fit residues: 141.4252 Evaluate side-chains 163 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 4.010 ------------------------------------------------------------------------------- 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 A residue 109 ILE Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 977 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 397 optimal weight: 5.9990 chunk 393 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 406 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 282 optimal weight: 8.9990 chunk 229 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 111 optimal weight: 0.0570 chunk 171 optimal weight: 0.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** I 632 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.068767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.050745 restraints weight = 84713.684| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.32 r_work: 0.2640 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 33870 Z= 0.239 Angle : 0.585 9.629 45972 Z= 0.309 Chirality : 0.046 0.157 4848 Planarity : 0.004 0.050 5976 Dihedral : 6.202 59.128 5014 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.18 % Favored : 95.63 % Rotamer: Outliers : 0.69 % Allowed : 5.38 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.13), residues: 4118 helix: 1.43 (0.20), residues: 720 sheet: 0.48 (0.15), residues: 1242 loop : -0.42 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 36 HIS 0.004 0.001 HIS M 71 PHE 0.017 0.001 PHE B 342 TYR 0.016 0.002 TYR A 225 ARG 0.012 0.001 ARG M 245 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01150 ( 16) link_ALPHA2-6 : angle 2.73824 ( 48) hydrogen bonds : bond 0.03947 ( 1420) hydrogen bonds : angle 4.91049 ( 3909) SS BOND : bond 0.00115 ( 2) SS BOND : angle 5.70012 ( 4) glycosidic custom : bond 0.00932 ( 2) glycosidic custom : angle 2.46164 ( 6) covalent geometry : bond 0.00544 (33850) covalent geometry : angle 0.57585 (45914) *********************** 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 183 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 3.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 216 MET cc_start: 0.6930 (mmm) cc_final: 0.6464 (mmm) REVERT: E 276 MET cc_start: 0.8154 (mmm) cc_final: 0.7669 (mmt) REVERT: T 49 MET cc_start: 0.8277 (mpp) cc_final: 0.7518 (mpp) REVERT: M 356 MET cc_start: 0.9140 (mmm) cc_final: 0.8817 (mmm) REVERT: G 30 ASP cc_start: 0.8559 (t0) cc_final: 0.8217 (t0) REVERT: G 48 ARG cc_start: 0.8416 (mmm160) cc_final: 0.8110 (mmm160) REVERT: G 49 MET cc_start: 0.8084 (mpp) cc_final: 0.7087 (mpp) REVERT: G 94 LYS cc_start: 0.9039 (ptpp) cc_final: 0.8698 (ptpp) REVERT: B 7 ARG cc_start: 0.7963 (ttm170) cc_final: 0.7599 (mtp180) REVERT: A 108 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: I 108 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8322 (pm20) REVERT: I 777 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8470 (tt0) outliers start: 24 outliers final: 13 residues processed: 172 average time/residue: 0.4436 time to fit residues: 126.7489 Evaluate side-chains 163 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 3.495 ------------------------------------------------------------------------------- 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 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 312 VAL Chi-restraints excluded: chain A residue 496 LEU 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 496 LEU 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 260 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 163 optimal weight: 0.0870 chunk 287 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 334 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 173 optimal weight: 4.9990 chunk 384 optimal weight: 4.9990 chunk 324 optimal weight: 0.7980 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 468 GLN J 43 ASN I 632 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.069752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.051787 restraints weight = 84329.509| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.34 r_work: 0.2662 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33870 Z= 0.159 Angle : 0.513 9.387 45972 Z= 0.271 Chirality : 0.044 0.188 4848 Planarity : 0.003 0.037 5976 Dihedral : 5.579 59.940 5014 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.57 % Favored : 96.26 % Rotamer: Outliers : 0.75 % Allowed : 6.56 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.13), residues: 4118 helix: 1.53 (0.20), residues: 710 sheet: 0.42 (0.15), residues: 1262 loop : -0.38 (0.14), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 91 HIS 0.004 0.001 HIS E 71 PHE 0.011 0.001 PHE B 342 TYR 0.016 0.001 TYR J 203 ARG 0.006 0.000 ARG M 245 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01158 ( 16) link_ALPHA2-6 : angle 2.67290 ( 48) hydrogen bonds : bond 0.03414 ( 1420) hydrogen bonds : angle 4.72796 ( 3909) SS BOND : bond 0.00843 ( 2) SS BOND : angle 2.68621 ( 4) glycosidic custom : bond 0.01034 ( 2) glycosidic custom : angle 2.44287 ( 6) covalent geometry : bond 0.00358 (33850) covalent geometry : angle 0.50448 (45914) *********************** 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 180 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 3.470 Fit side-chains revert: symmetry clash REVERT: T 49 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7526 (mpp) REVERT: M 356 MET cc_start: 0.9156 (mmm) cc_final: 0.8812 (mmm) REVERT: G 30 ASP cc_start: 0.8588 (t0) cc_final: 0.8247 (t0) REVERT: G 56 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7386 (mt) REVERT: G 94 LYS cc_start: 0.9075 (ptpp) cc_final: 0.8735 (ptpp) REVERT: B 389 CYS cc_start: 0.6897 (m) cc_final: 0.6627 (m) REVERT: A 108 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8251 (pm20) REVERT: J 111 MET cc_start: 0.9155 (ttm) cc_final: 0.8864 (ttm) REVERT: J 389 CYS cc_start: 0.6814 (m) cc_final: 0.6569 (m) REVERT: I 108 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8311 (pm20) REVERT: I 777 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8477 (tt0) outliers start: 26 outliers final: 15 residues processed: 172 average time/residue: 0.4303 time to fit residues: 124.1435 Evaluate side-chains 167 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 3.490 ------------------------------------------------------------------------------- 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 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 109 ILE Chi-restraints excluded: chain A residue 496 LEU 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 445 MET Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 509 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 134 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 286 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 265 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 264 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.067972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.050040 restraints weight = 85040.429| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.33 r_work: 0.2617 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 33870 Z= 0.240 Angle : 0.557 9.293 45972 Z= 0.294 Chirality : 0.045 0.185 4848 Planarity : 0.004 0.046 5976 Dihedral : 5.429 59.320 5014 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.25 % Favored : 95.58 % Rotamer: Outliers : 1.06 % Allowed : 7.22 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.13), residues: 4118 helix: 1.41 (0.20), residues: 720 sheet: 0.32 (0.15), residues: 1252 loop : -0.44 (0.14), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 36 HIS 0.004 0.001 HIS M 71 PHE 0.015 0.001 PHE J 342 TYR 0.021 0.001 TYR J 203 ARG 0.019 0.001 ARG M 245 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01049 ( 16) link_ALPHA2-6 : angle 2.73866 ( 48) hydrogen bonds : bond 0.03807 ( 1420) hydrogen bonds : angle 4.88354 ( 3909) SS BOND : bond 0.00796 ( 2) SS BOND : angle 2.26669 ( 4) glycosidic custom : bond 0.01203 ( 2) glycosidic custom : angle 2.18053 ( 6) covalent geometry : bond 0.00547 (33850) covalent geometry : angle 0.54951 (45914) *********************** 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 186 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 3.920 Fit side-chains REVERT: E 44 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8110 (mpp) REVERT: E 276 MET cc_start: 0.8189 (mmm) cc_final: 0.7882 (mmt) REVERT: T 49 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7389 (mpp) REVERT: T 56 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7332 (mt) REVERT: M 183 MET cc_start: 0.9254 (ttp) cc_final: 0.8816 (ttm) REVERT: M 244 MET cc_start: 0.8881 (tpp) cc_final: 0.8606 (tpp) REVERT: M 356 MET cc_start: 0.9139 (mmm) cc_final: 0.8799 (mmm) REVERT: G 30 ASP cc_start: 0.8608 (t0) cc_final: 0.8273 (t0) REVERT: G 48 ARG cc_start: 0.8417 (mmm160) cc_final: 0.8116 (mmm-85) REVERT: G 49 MET cc_start: 0.8518 (mpp) cc_final: 0.7457 (mpp) REVERT: G 56 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7617 (mt) REVERT: B 7 ARG cc_start: 0.7931 (ttm170) cc_final: 0.7651 (mtp180) REVERT: A 108 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8189 (pm20) REVERT: J 111 MET cc_start: 0.9169 (ttm) cc_final: 0.8795 (ttm) REVERT: I 108 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8272 (pm20) REVERT: I 777 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8509 (tt0) outliers start: 37 outliers final: 25 residues processed: 175 average time/residue: 0.4340 time to fit residues: 128.0286 Evaluate side-chains 176 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 3.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET 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 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 213 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 88 SER 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 496 LEU 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 496 LEU 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 120 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 363 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 199 optimal weight: 2.9990 chunk 307 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 163 optimal weight: 0.0770 chunk 32 optimal weight: 7.9990 chunk 249 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.069845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.052416 restraints weight = 84204.701| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.34 r_work: 0.2671 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1982 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= 0.138 Angle : 0.506 12.821 45972 Z= 0.267 Chirality : 0.043 0.206 4848 Planarity : 0.003 0.038 5976 Dihedral : 5.059 57.412 5014 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.30 % Favored : 96.53 % Rotamer: Outliers : 1.01 % Allowed : 7.59 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.13), residues: 4118 helix: 1.45 (0.20), residues: 722 sheet: 0.36 (0.15), residues: 1262 loop : -0.37 (0.14), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 486 HIS 0.003 0.001 HIS E 71 PHE 0.011 0.001 PHE J 301 TYR 0.016 0.001 TYR B 203 ARG 0.003 0.000 ARG T 95 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01169 ( 16) link_ALPHA2-6 : angle 2.68131 ( 48) hydrogen bonds : bond 0.03300 ( 1420) hydrogen bonds : angle 4.70269 ( 3909) SS BOND : bond 0.00408 ( 2) SS BOND : angle 3.83499 ( 4) glycosidic custom : bond 0.01325 ( 2) glycosidic custom : angle 2.15459 ( 6) covalent geometry : bond 0.00307 (33850) covalent geometry : angle 0.49688 (45914) *********************** 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 184 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 3.815 Fit side-chains revert: symmetry clash REVERT: E 44 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8110 (mpp) REVERT: E 244 MET cc_start: 0.8700 (tpp) cc_final: 0.8425 (tpp) REVERT: T 49 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7374 (mpp) REVERT: T 56 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7147 (mt) REVERT: M 156 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8532 (tt) REVERT: M 183 MET cc_start: 0.9249 (ttp) cc_final: 0.8876 (ttm) REVERT: M 356 MET cc_start: 0.9126 (mmm) cc_final: 0.8766 (mmm) REVERT: G 19 SER cc_start: 0.8989 (m) cc_final: 0.8545 (p) REVERT: G 30 ASP cc_start: 0.8573 (t0) cc_final: 0.8223 (t0) REVERT: G 94 LYS cc_start: 0.8979 (ptpp) cc_final: 0.8649 (ptpp) REVERT: A 108 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8270 (pm20) REVERT: J 111 MET cc_start: 0.9043 (ttm) cc_final: 0.8704 (ttm) REVERT: J 288 MET cc_start: 0.9386 (mmt) cc_final: 0.9062 (mmt) REVERT: I 108 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8426 (pm20) REVERT: I 777 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8410 (tm-30) outliers start: 35 outliers final: 20 residues processed: 173 average time/residue: 0.4244 time to fit residues: 125.2092 Evaluate side-chains 171 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 3.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET 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 147 THR 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 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 496 LEU 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 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 272 optimal weight: 4.9990 chunk 381 optimal weight: 0.7980 chunk 182 optimal weight: 10.0000 chunk 348 optimal weight: 10.0000 chunk 302 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 245 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.068908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.051252 restraints weight = 84587.600| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.34 r_work: 0.2648 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33870 Z= 0.197 Angle : 0.535 12.113 45972 Z= 0.281 Chirality : 0.044 0.221 4848 Planarity : 0.003 0.038 5976 Dihedral : 5.010 58.058 5014 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.03 % Favored : 95.82 % Rotamer: Outliers : 1.04 % Allowed : 7.79 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.13), residues: 4118 helix: 1.42 (0.20), residues: 722 sheet: 0.44 (0.15), residues: 1230 loop : -0.43 (0.14), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 486 HIS 0.004 0.001 HIS E 71 PHE 0.013 0.001 PHE J 342 TYR 0.023 0.001 TYR G 42 ARG 0.005 0.000 ARG T 10 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01052 ( 16) link_ALPHA2-6 : angle 2.77721 ( 48) hydrogen bonds : bond 0.03523 ( 1420) hydrogen bonds : angle 4.74181 ( 3909) SS BOND : bond 0.00703 ( 2) SS BOND : angle 5.50521 ( 4) glycosidic custom : bond 0.01321 ( 2) glycosidic custom : angle 2.13153 ( 6) covalent geometry : bond 0.00448 (33850) covalent geometry : angle 0.52497 (45914) *********************** 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 184 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 3.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8147 (mpp) REVERT: E 244 MET cc_start: 0.8795 (tpp) cc_final: 0.8337 (tpp) REVERT: E 276 MET cc_start: 0.7846 (mmm) cc_final: 0.7402 (mmt) REVERT: T 49 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7329 (mpp) REVERT: T 56 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7121 (mt) REVERT: M 156 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8517 (tt) REVERT: M 183 MET cc_start: 0.9261 (ttp) cc_final: 0.8901 (ttm) REVERT: M 356 MET cc_start: 0.9117 (mmm) cc_final: 0.8757 (mmm) REVERT: G 19 SER cc_start: 0.9008 (m) cc_final: 0.8533 (p) REVERT: G 30 ASP cc_start: 0.8582 (t0) cc_final: 0.8205 (t0) REVERT: G 48 ARG cc_start: 0.8718 (mmm-85) cc_final: 0.8276 (mmm160) REVERT: G 49 MET cc_start: 0.8470 (mpp) cc_final: 0.7347 (mpp) REVERT: G 56 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7377 (mt) REVERT: G 94 LYS cc_start: 0.8981 (ptpp) cc_final: 0.8646 (ptpp) REVERT: A 108 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8253 (pm20) REVERT: J 111 MET cc_start: 0.9038 (ttm) cc_final: 0.8701 (ttm) REVERT: I 108 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8288 (pm20) REVERT: I 777 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8433 (tm-30) outliers start: 36 outliers final: 24 residues processed: 171 average time/residue: 0.4542 time to fit residues: 132.0949 Evaluate side-chains 177 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 3.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET 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 147 THR Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain G residue 11 LEU 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 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 496 LEU 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 496 LEU Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 321 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 206 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 382 optimal weight: 7.9990 chunk 272 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 309 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.068761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.051040 restraints weight = 84270.650| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.40 r_work: 0.2644 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 33870 Z= 0.199 Angle : 0.532 11.348 45972 Z= 0.280 Chirality : 0.044 0.222 4848 Planarity : 0.003 0.038 5976 Dihedral : 4.974 55.958 5014 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.59 % Favored : 96.28 % Rotamer: Outliers : 1.04 % Allowed : 7.94 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.13), residues: 4118 helix: 1.40 (0.20), residues: 722 sheet: 0.35 (0.15), residues: 1254 loop : -0.45 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 486 HIS 0.004 0.001 HIS E 71 PHE 0.012 0.001 PHE J 342 TYR 0.024 0.001 TYR T 42 ARG 0.004 0.000 ARG M 245 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01061 ( 16) link_ALPHA2-6 : angle 2.84077 ( 48) hydrogen bonds : bond 0.03516 ( 1420) hydrogen bonds : angle 4.74623 ( 3909) SS BOND : bond 0.00725 ( 2) SS BOND : angle 4.62461 ( 4) glycosidic custom : bond 0.01366 ( 2) glycosidic custom : angle 2.06720 ( 6) covalent geometry : bond 0.00454 (33850) covalent geometry : angle 0.52226 (45914) *********************** 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 183 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 3.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8216 (mpp) REVERT: E 244 MET cc_start: 0.8789 (tpp) cc_final: 0.8326 (tpp) REVERT: E 276 MET cc_start: 0.7912 (mmm) cc_final: 0.7360 (mmt) REVERT: T 19 SER cc_start: 0.8940 (m) cc_final: 0.8498 (p) REVERT: T 49 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7332 (mpp) REVERT: T 56 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7145 (mt) REVERT: M 156 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8530 (tt) REVERT: M 183 MET cc_start: 0.9256 (ttp) cc_final: 0.8909 (ttm) REVERT: M 229 MET cc_start: 0.8697 (tpp) cc_final: 0.8220 (ttm) REVERT: G 19 SER cc_start: 0.8995 (m) cc_final: 0.8519 (p) REVERT: G 30 ASP cc_start: 0.8598 (t0) cc_final: 0.8206 (t0) REVERT: G 56 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7377 (mt) REVERT: G 94 LYS cc_start: 0.8984 (ptpp) cc_final: 0.8651 (ptpp) REVERT: A 108 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8131 (pm20) REVERT: J 111 MET cc_start: 0.9050 (ttm) cc_final: 0.8725 (ttm) REVERT: I 108 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8416 (pm20) REVERT: I 777 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8455 (tm-30) outliers start: 36 outliers final: 25 residues processed: 167 average time/residue: 0.4318 time to fit residues: 122.7704 Evaluate side-chains 176 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 183 MET 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 147 THR Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain G residue 11 LEU 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 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 496 LEU 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 496 LEU Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 77 optimal weight: 3.9990 chunk 390 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 341 optimal weight: 0.7980 chunk 331 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 333 optimal weight: 4.9990 chunk 379 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 352 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.068590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.050996 restraints weight = 84307.751| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 2.35 r_work: 0.2643 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 33870 Z= 0.198 Angle : 0.532 10.282 45972 Z= 0.279 Chirality : 0.044 0.230 4848 Planarity : 0.003 0.038 5976 Dihedral : 4.924 51.909 5014 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 1.04 % Allowed : 8.05 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.13), residues: 4118 helix: 1.37 (0.20), residues: 722 sheet: 0.35 (0.15), residues: 1254 loop : -0.45 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 486 HIS 0.005 0.001 HIS E 71 PHE 0.013 0.001 PHE J 342 TYR 0.019 0.001 TYR T 42 ARG 0.003 0.000 ARG E 294 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01045 ( 16) link_ALPHA2-6 : angle 2.86562 ( 48) hydrogen bonds : bond 0.03510 ( 1420) hydrogen bonds : angle 4.74286 ( 3909) SS BOND : bond 0.00722 ( 2) SS BOND : angle 4.17281 ( 4) glycosidic custom : bond 0.01352 ( 2) glycosidic custom : angle 2.05314 ( 6) covalent geometry : bond 0.00450 (33850) covalent geometry : angle 0.52184 (45914) *********************** 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 182 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8240 (mpp) REVERT: E 244 MET cc_start: 0.8802 (tpp) cc_final: 0.8333 (tpp) REVERT: E 276 MET cc_start: 0.7920 (mmm) cc_final: 0.7390 (mmt) REVERT: T 19 SER cc_start: 0.8935 (m) cc_final: 0.8499 (p) REVERT: T 49 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7359 (mpp) REVERT: T 53 GLU cc_start: 0.8375 (pp20) cc_final: 0.8051 (pp20) REVERT: T 56 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7122 (mt) REVERT: M 156 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8496 (tt) REVERT: M 183 MET cc_start: 0.9301 (ttp) cc_final: 0.8984 (ttm) REVERT: M 229 MET cc_start: 0.8689 (tpp) cc_final: 0.8215 (ttm) REVERT: M 276 MET cc_start: 0.7706 (mmm) cc_final: 0.7040 (mmt) REVERT: G 19 SER cc_start: 0.8979 (m) cc_final: 0.8497 (p) REVERT: G 30 ASP cc_start: 0.8595 (t0) cc_final: 0.8204 (t0) REVERT: G 56 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7424 (mt) REVERT: G 94 LYS cc_start: 0.8989 (ptpp) cc_final: 0.8659 (ptpp) REVERT: A 108 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8077 (pm20) REVERT: A 506 MET cc_start: 0.8871 (tmm) cc_final: 0.8650 (tmm) REVERT: J 111 MET cc_start: 0.9044 (ttm) cc_final: 0.8652 (ttm) REVERT: I 108 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8406 (pm20) REVERT: I 777 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8447 (tm-30) REVERT: I 968 MET cc_start: 0.8265 (ttm) cc_final: 0.8050 (ttm) outliers start: 36 outliers final: 26 residues processed: 169 average time/residue: 0.4171 time to fit residues: 119.1523 Evaluate side-chains 178 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET 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 147 THR 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 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 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 496 LEU 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 496 LEU 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 142 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 361 optimal weight: 0.6980 chunk 260 optimal weight: 0.7980 chunk 372 optimal weight: 0.3980 chunk 208 optimal weight: 0.9990 chunk 360 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 218 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** A 677 GLN I 151 ASN I 677 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.070241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.052606 restraints weight = 84002.019| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.42 r_work: 0.2681 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 33870 Z= 0.108 Angle : 0.497 16.323 45972 Z= 0.260 Chirality : 0.043 0.222 4848 Planarity : 0.003 0.039 5976 Dihedral : 4.625 53.004 5014 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.30 % Favored : 96.62 % Rotamer: Outliers : 0.98 % Allowed : 8.25 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.13), residues: 4118 helix: 1.39 (0.20), residues: 732 sheet: 0.41 (0.15), residues: 1246 loop : -0.38 (0.14), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 486 HIS 0.004 0.001 HIS E 71 PHE 0.011 0.001 PHE J 301 TYR 0.019 0.001 TYR T 42 ARG 0.003 0.000 ARG M 294 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01179 ( 16) link_ALPHA2-6 : angle 2.76971 ( 48) hydrogen bonds : bond 0.03033 ( 1420) hydrogen bonds : angle 4.52386 ( 3909) SS BOND : bond 0.00436 ( 2) SS BOND : angle 3.76108 ( 4) glycosidic custom : bond 0.01387 ( 2) glycosidic custom : angle 2.08446 ( 6) covalent geometry : bond 0.00234 (33850) covalent geometry : angle 0.48686 (45914) ********************** 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 187 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 3.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8076 (mpp) REVERT: E 276 MET cc_start: 0.7820 (mmm) cc_final: 0.7328 (mmt) REVERT: T 19 SER cc_start: 0.8986 (m) cc_final: 0.8562 (p) REVERT: T 49 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7951 (mpp) REVERT: M 156 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8440 (tt) REVERT: M 183 MET cc_start: 0.9330 (ttp) cc_final: 0.9028 (ttm) REVERT: M 229 MET cc_start: 0.8714 (tpp) cc_final: 0.8267 (ttm) REVERT: M 276 MET cc_start: 0.7767 (mmm) cc_final: 0.7001 (mmt) REVERT: G 19 SER cc_start: 0.8966 (m) cc_final: 0.8528 (p) REVERT: G 30 ASP cc_start: 0.8633 (t0) cc_final: 0.8390 (t0) REVERT: G 48 ARG cc_start: 0.8345 (mmm160) cc_final: 0.7971 (mmm160) REVERT: G 49 MET cc_start: 0.8452 (mpp) cc_final: 0.7380 (mpp) REVERT: G 56 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7447 (mt) REVERT: G 94 LYS cc_start: 0.8959 (ptpp) cc_final: 0.8627 (ptpp) REVERT: A 108 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8062 (pm20) REVERT: A 506 MET cc_start: 0.8860 (tmm) cc_final: 0.8658 (tmm) REVERT: J 111 MET cc_start: 0.9008 (ttm) cc_final: 0.8635 (ttm) REVERT: I 108 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8409 (pm20) REVERT: I 496 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8459 (mt) REVERT: I 777 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8423 (tm-30) outliers start: 34 outliers final: 20 residues processed: 175 average time/residue: 0.4391 time to fit residues: 129.5591 Evaluate side-chains 176 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET 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 M residue 56 VAL 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 156 LEU 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 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 356 ILE Chi-restraints excluded: chain I residue 427 MET Chi-restraints excluded: chain I residue 496 LEU Chi-restraints excluded: chain I residue 509 MET 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 361 optimal weight: 3.9990 chunk 315 optimal weight: 0.0020 chunk 137 optimal weight: 6.9990 chunk 376 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 chunk 230 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 344 optimal weight: 5.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.068583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.050955 restraints weight = 84697.678| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 2.36 r_work: 0.2642 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 33870 Z= 0.212 Angle : 0.542 15.888 45972 Z= 0.283 Chirality : 0.044 0.253 4848 Planarity : 0.003 0.041 5976 Dihedral : 4.774 46.709 5014 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.08 % Favored : 95.85 % Rotamer: Outliers : 0.89 % Allowed : 8.34 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.13), residues: 4118 helix: 1.31 (0.20), residues: 734 sheet: 0.36 (0.15), residues: 1256 loop : -0.44 (0.14), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 36 HIS 0.003 0.001 HIS B 132 PHE 0.013 0.001 PHE J 342 TYR 0.021 0.001 TYR B 203 ARG 0.003 0.000 ARG J 515 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01023 ( 16) link_ALPHA2-6 : angle 2.92873 ( 48) hydrogen bonds : bond 0.03489 ( 1420) hydrogen bonds : angle 4.69083 ( 3909) SS BOND : bond 0.00632 ( 2) SS BOND : angle 3.68123 ( 4) glycosidic custom : bond 0.01275 ( 2) glycosidic custom : angle 2.04689 ( 6) covalent geometry : bond 0.00484 (33850) covalent geometry : angle 0.53248 (45914) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15048.93 seconds wall clock time: 262 minutes 11.99 seconds (15731.99 seconds total)