Starting phenix.real_space_refine on Sat Jun 28 12:00:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aa0_15289/06_2025/8aa0_15289.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aa0_15289/06_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_15289/06_2025/8aa0_15289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aa0_15289/06_2025/8aa0_15289.map" model { file = "/net/cci-nas-00/data/ceres_data/8aa0_15289/06_2025/8aa0_15289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aa0_15289/06_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-5710/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: 18.23, per 1000 atoms: 0.55 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: 8.37 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: 5.34 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: 17.43 Time building geometry restraints manager: 9.91 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.410 Check model and map are aligned: 0.220 Set scattering table: 0.310 Process input model: 79.480 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.200 ------------------------------------------------------------------------------- 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 : 3.828 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: 0.4590 time to fit residues: 152.2640 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 : 3.734 ------------------------------------------------------------------------------- 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 = 0.072777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.054730 restraints weight = 83913.990| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.34 r_work: 0.2744 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 : 0.523 8.108 45972 Z= 0.275 Chirality : 0.043 0.163 4848 Planarity : 0.003 0.039 5976 Dihedral : 7.947 53.639 5014 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.36 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 A 225 ARG 0.004 0.000 ARG G 21 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01266 ( 16) link_ALPHA2-6 : angle 3.00079 ( 48) hydrogen bonds : bond 0.03412 ( 1420) hydrogen bonds : angle 4.79022 ( 3909) SS BOND : bond 0.01105 ( 2) SS BOND : angle 0.14422 ( 4) glycosidic custom : bond 0.00795 ( 2) glycosidic custom : angle 2.90294 ( 6) covalent geometry : bond 0.00243 (33850) covalent geometry : angle 0.51320 (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 : 4.746 Fit side-chains revert: symmetry clash REVERT: E 215 MET cc_start: 0.7835 (mtt) cc_final: 0.7438 (mtt) REVERT: E 216 MET cc_start: 0.6716 (mmm) cc_final: 0.6329 (mmm) REVERT: E 276 MET cc_start: 0.8127 (mmm) cc_final: 0.7657 (mmt) REVERT: T 10 ARG cc_start: 0.9027 (ptp90) cc_final: 0.8777 (ptp90) REVERT: M 44 MET cc_start: 0.8851 (mtt) cc_final: 0.8539 (mtt) REVERT: M 356 MET cc_start: 0.9130 (mmm) cc_final: 0.8838 (mmm) REVERT: G 30 ASP cc_start: 0.8438 (t0) cc_final: 0.8072 (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: 0.6124 time to fit residues: 188.0186 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 : 3.769 ------------------------------------------------------------------------------- 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: 0.6980 chunk 393 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 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: 0.0970 chunk 171 optimal weight: 0.4980 overall best weight: 1.8582 ------------------------------------------------------------------------------- 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** B 302 HIS J 43 ASN I 632 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.070910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.052870 restraints weight = 84399.478| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.35 r_work: 0.2691 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33870 Z= 0.162 Angle : 0.526 9.703 45972 Z= 0.277 Chirality : 0.044 0.193 4848 Planarity : 0.003 0.038 5976 Dihedral : 5.986 55.048 5014 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.91 % Favored : 95.90 % Rotamer: Outliers : 0.69 % Allowed : 5.00 % Favored : 94.31 % 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: 0.36 (0.13), residues: 4118 helix: 1.57 (0.20), residues: 722 sheet: 0.50 (0.15), residues: 1266 loop : -0.34 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 36 HIS 0.004 0.001 HIS J 302 PHE 0.013 0.001 PHE B 342 TYR 0.021 0.001 TYR G 42 ARG 0.006 0.000 ARG M 245 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01297 ( 16) link_ALPHA2-6 : angle 2.74001 ( 48) hydrogen bonds : bond 0.03437 ( 1420) hydrogen bonds : angle 4.68015 ( 3909) SS BOND : bond 0.01396 ( 2) SS BOND : angle 4.27288 ( 4) glycosidic custom : bond 0.01114 ( 2) glycosidic custom : angle 2.60858 ( 6) covalent geometry : bond 0.00360 (33850) covalent geometry : angle 0.51666 (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 189 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 3.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 215 MET cc_start: 0.8140 (mtt) cc_final: 0.7683 (mtt) REVERT: E 216 MET cc_start: 0.6878 (mmm) cc_final: 0.6498 (mmm) REVERT: E 276 MET cc_start: 0.8156 (mmm) cc_final: 0.7672 (mmt) REVERT: T 21 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8280 (ttm-80) REVERT: T 30 ASP cc_start: 0.8740 (t0) cc_final: 0.8277 (p0) REVERT: T 49 MET cc_start: 0.8279 (mpp) cc_final: 0.7591 (mpp) REVERT: M 356 MET cc_start: 0.9163 (mmm) cc_final: 0.8840 (mmm) REVERT: G 30 ASP cc_start: 0.8513 (t0) cc_final: 0.8210 (t0) REVERT: G 94 LYS cc_start: 0.9034 (ptpp) cc_final: 0.8686 (ptpp) REVERT: I 108 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8392 (pm20) outliers start: 24 outliers final: 11 residues processed: 177 average time/residue: 0.4688 time to fit residues: 139.0961 Evaluate side-chains 169 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 109 ILE 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 496 LEU Chi-restraints excluded: chain I residue 509 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 260 optimal weight: 8.9990 chunk 246 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 244 optimal weight: 0.0970 chunk 334 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 173 optimal weight: 0.0470 chunk 384 optimal weight: 9.9990 chunk 324 optimal weight: 0.9980 overall best weight: 2.2280 ------------------------------------------------------------------------------- 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 468 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.069897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.051971 restraints weight = 84471.008| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.31 r_work: 0.2665 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1544 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= 0.176 Angle : 0.523 13.677 45972 Z= 0.276 Chirality : 0.044 0.188 4848 Planarity : 0.003 0.036 5976 Dihedral : 5.349 48.779 5014 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.59 % Favored : 96.24 % Rotamer: Outliers : 0.66 % Allowed : 6.53 % Favored : 92.81 % 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: 0.30 (0.13), residues: 4118 helix: 1.50 (0.20), residues: 722 sheet: 0.44 (0.15), residues: 1270 loop : -0.35 (0.14), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.004 0.001 HIS M 71 PHE 0.013 0.001 PHE B 342 TYR 0.016 0.001 TYR J 203 ARG 0.006 0.001 ARG G 95 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01117 ( 16) link_ALPHA2-6 : angle 2.70767 ( 48) hydrogen bonds : bond 0.03429 ( 1420) hydrogen bonds : angle 4.65295 ( 3909) SS BOND : bond 0.00851 ( 2) SS BOND : angle 3.38298 ( 4) glycosidic custom : bond 0.01036 ( 2) glycosidic custom : angle 2.41066 ( 6) covalent geometry : bond 0.00399 (33850) covalent geometry : angle 0.51420 (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: 23 poor density : 157 time to evaluate : 4.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 215 MET cc_start: 0.8132 (mtt) cc_final: 0.7636 (mtt) REVERT: T 49 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7541 (mpp) REVERT: M 356 MET cc_start: 0.9168 (mmm) cc_final: 0.8809 (mmm) REVERT: G 19 SER cc_start: 0.8938 (m) cc_final: 0.8535 (p) REVERT: G 30 ASP cc_start: 0.8562 (t0) cc_final: 0.8218 (t0) REVERT: G 56 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7356 (mt) REVERT: B 389 CYS cc_start: 0.6889 (m) cc_final: 0.6652 (m) REVERT: I 108 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8304 (pm20) REVERT: I 427 MET cc_start: 0.8243 (mtm) cc_final: 0.7949 (mtt) REVERT: I 777 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8476 (tt0) outliers start: 23 outliers final: 14 residues processed: 173 average time/residue: 0.5223 time to fit residues: 153.2879 Evaluate side-chains 168 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 4.322 ------------------------------------------------------------------------------- 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 109 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 134 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 204 optimal weight: 0.9990 chunk 286 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 265 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 132 optimal weight: 0.0270 chunk 264 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 overall best weight: 3.0046 ------------------------------------------------------------------------------- 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 309 ASN A 864 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.068340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.050447 restraints weight = 85128.972| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.31 r_work: 0.2627 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 33870 Z= 0.230 Angle : 0.551 10.522 45972 Z= 0.292 Chirality : 0.045 0.197 4848 Planarity : 0.004 0.046 5976 Dihedral : 5.236 59.177 5014 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.98 % Favored : 95.85 % Rotamer: Outliers : 0.95 % Allowed : 6.96 % Favored : 92.09 % 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: 1.50 (0.20), residues: 720 sheet: 0.38 (0.15), residues: 1260 loop : -0.40 (0.14), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 36 HIS 0.004 0.001 HIS B 343 PHE 0.015 0.001 PHE B 342 TYR 0.021 0.001 TYR J 203 ARG 0.015 0.001 ARG M 245 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01055 ( 16) link_ALPHA2-6 : angle 2.73547 ( 48) hydrogen bonds : bond 0.03728 ( 1420) hydrogen bonds : angle 4.79837 ( 3909) SS BOND : bond 0.00839 ( 2) SS BOND : angle 2.35050 ( 4) glycosidic custom : bond 0.01270 ( 2) glycosidic custom : angle 2.14902 ( 6) covalent geometry : bond 0.00525 (33850) covalent geometry : angle 0.54345 (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 183 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 3.606 Fit side-chains revert: symmetry clash REVERT: E 215 MET cc_start: 0.8179 (mtt) cc_final: 0.7706 (mtt) REVERT: E 216 MET cc_start: 0.7261 (mmm) cc_final: 0.6996 (mmm) REVERT: E 276 MET cc_start: 0.8212 (mmm) cc_final: 0.7774 (mmt) REVERT: T 49 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7359 (mpp) REVERT: T 56 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7336 (mt) REVERT: M 183 MET cc_start: 0.9260 (ttp) cc_final: 0.8846 (ttm) REVERT: M 244 MET cc_start: 0.8868 (tpp) cc_final: 0.8629 (tpp) REVERT: M 356 MET cc_start: 0.9160 (mmm) cc_final: 0.8810 (mmm) REVERT: G 30 ASP cc_start: 0.8630 (t0) cc_final: 0.8309 (t0) REVERT: G 48 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.8536 (mmm-85) REVERT: G 49 MET cc_start: 0.8610 (mpp) cc_final: 0.7487 (mpp) REVERT: G 56 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7610 (mt) REVERT: B 7 ARG cc_start: 0.7941 (ttm170) cc_final: 0.7646 (mtp180) REVERT: I 108 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8278 (pm20) REVERT: I 777 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8515 (tt0) outliers start: 33 outliers final: 23 residues processed: 172 average time/residue: 0.4451 time to fit residues: 127.6721 Evaluate side-chains 170 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain 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 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 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: 0.5980 chunk 31 optimal weight: 3.9990 chunk 363 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 307 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 163 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.068952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.051326 restraints weight = 84707.364| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.33 r_work: 0.2651 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 33870 Z= 0.199 Angle : 0.526 10.413 45972 Z= 0.278 Chirality : 0.044 0.200 4848 Planarity : 0.003 0.038 5976 Dihedral : 5.080 56.506 5014 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.57 % Favored : 96.26 % Rotamer: Outliers : 1.06 % Allowed : 7.45 % Favored : 91.49 % 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: 0.18 (0.13), residues: 4118 helix: 1.45 (0.20), residues: 720 sheet: 0.30 (0.14), residues: 1268 loop : -0.40 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 486 HIS 0.004 0.001 HIS E 71 PHE 0.012 0.001 PHE J 342 TYR 0.024 0.001 TYR G 42 ARG 0.006 0.000 ARG T 10 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01068 ( 16) link_ALPHA2-6 : angle 2.76995 ( 48) hydrogen bonds : bond 0.03522 ( 1420) hydrogen bonds : angle 4.74803 ( 3909) SS BOND : bond 0.00679 ( 2) SS BOND : angle 0.74712 ( 4) glycosidic custom : bond 0.01323 ( 2) glycosidic custom : angle 2.11548 ( 6) covalent geometry : bond 0.00452 (33850) covalent geometry : angle 0.51836 (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 183 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 3.944 Fit side-chains REVERT: T 49 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7241 (mpp) REVERT: T 56 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7118 (mt) REVERT: M 156 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8567 (tt) REVERT: M 183 MET cc_start: 0.9254 (ttp) cc_final: 0.8890 (ttm) REVERT: M 356 MET cc_start: 0.9120 (mmm) cc_final: 0.8757 (mmm) REVERT: G 30 ASP cc_start: 0.8579 (t0) cc_final: 0.8206 (t0) REVERT: G 48 ARG cc_start: 0.8753 (mmm-85) cc_final: 0.8500 (mmm-85) REVERT: G 49 MET cc_start: 0.8454 (mpp) cc_final: 0.7282 (mpp) REVERT: G 56 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7467 (mt) REVERT: I 108 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8293 (pm20) REVERT: I 506 MET cc_start: 0.8890 (tmm) cc_final: 0.8679 (tmm) REVERT: I 777 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8477 (tt0) outliers start: 37 outliers final: 23 residues processed: 172 average time/residue: 0.4449 time to fit residues: 130.5298 Evaluate side-chains 170 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 3.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 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 445 MET Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 312 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 272 optimal weight: 2.9990 chunk 381 optimal weight: 6.9990 chunk 182 optimal weight: 8.9990 chunk 348 optimal weight: 8.9990 chunk 302 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 chunk 245 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 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 = 0.3169 r_free = 0.3169 target = 0.068360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.050567 restraints weight = 84775.484| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.39 r_work: 0.2631 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2495 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 33870 Z= 0.237 Angle : 0.559 10.543 45972 Z= 0.294 Chirality : 0.045 0.216 4848 Planarity : 0.004 0.043 5976 Dihedral : 5.127 57.631 5014 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.10 % Favored : 95.75 % Rotamer: Outliers : 1.09 % Allowed : 7.59 % Favored : 91.32 % 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: 0.13 (0.13), residues: 4118 helix: 1.40 (0.20), residues: 720 sheet: 0.33 (0.15), residues: 1250 loop : -0.47 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 36 HIS 0.005 0.001 HIS E 71 PHE 0.014 0.001 PHE J 342 TYR 0.015 0.001 TYR I 422 ARG 0.004 0.000 ARG G 95 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01014 ( 16) link_ALPHA2-6 : angle 2.84964 ( 48) hydrogen bonds : bond 0.03704 ( 1420) hydrogen bonds : angle 4.81284 ( 3909) SS BOND : bond 0.01079 ( 2) SS BOND : angle 7.19449 ( 4) glycosidic custom : bond 0.01353 ( 2) glycosidic custom : angle 2.06825 ( 6) covalent geometry : bond 0.00542 (33850) covalent geometry : angle 0.54726 (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 182 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 4.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 215 MET cc_start: 0.8519 (mtt) cc_final: 0.8024 (mtt) REVERT: E 244 MET cc_start: 0.8781 (tpp) cc_final: 0.8434 (tpp) REVERT: E 276 MET cc_start: 0.8089 (mmm) cc_final: 0.7380 (mmt) REVERT: T 49 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7249 (mpp) REVERT: T 56 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7171 (mt) REVERT: M 156 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8532 (tt) REVERT: M 183 MET cc_start: 0.9258 (ttp) cc_final: 0.8914 (ttm) REVERT: M 216 MET cc_start: 0.7706 (mmm) cc_final: 0.7251 (mmm) REVERT: G 19 SER cc_start: 0.9028 (m) cc_final: 0.8568 (p) REVERT: G 30 ASP cc_start: 0.8591 (t0) cc_final: 0.8208 (t0) REVERT: G 56 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7439 (mt) REVERT: B 7 ARG cc_start: 0.7900 (ttm170) cc_final: 0.7628 (mtp180) REVERT: A 427 MET cc_start: 0.8613 (tpp) cc_final: 0.8348 (mpp) REVERT: I 108 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: I 506 MET cc_start: 0.8926 (tmm) cc_final: 0.8707 (tmm) REVERT: I 777 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8472 (tt0) REVERT: I 968 MET cc_start: 0.8310 (ttm) cc_final: 0.8082 (ttm) outliers start: 38 outliers final: 26 residues processed: 171 average time/residue: 0.4396 time to fit residues: 127.5281 Evaluate side-chains 172 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 3.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 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 347 MET Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 312 VAL 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 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 453 ASN 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: 0.9980 chunk 282 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 174 optimal weight: 0.9990 chunk 382 optimal weight: 0.0370 chunk 272 optimal weight: 0.9980 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 321 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 309 ASN ** I 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.070642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.053239 restraints weight = 83556.851| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.35 r_work: 0.2696 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33870 Z= 0.101 Angle : 0.496 12.279 45972 Z= 0.261 Chirality : 0.042 0.204 4848 Planarity : 0.003 0.039 5976 Dihedral : 4.750 59.981 5014 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.16 % Favored : 96.72 % Rotamer: Outliers : 0.66 % Allowed : 8.19 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.13), residues: 4118 helix: 1.51 (0.20), residues: 720 sheet: 0.38 (0.15), residues: 1258 loop : -0.35 (0.14), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 486 HIS 0.003 0.001 HIS B 132 PHE 0.014 0.001 PHE J 301 TYR 0.021 0.001 TYR T 42 ARG 0.004 0.000 ARG G 95 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01250 ( 16) link_ALPHA2-6 : angle 2.71868 ( 48) hydrogen bonds : bond 0.03015 ( 1420) hydrogen bonds : angle 4.52184 ( 3909) SS BOND : bond 0.00789 ( 2) SS BOND : angle 6.73798 ( 4) glycosidic custom : bond 0.01407 ( 2) glycosidic custom : angle 2.11505 ( 6) covalent geometry : bond 0.00212 (33850) covalent geometry : angle 0.48332 (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 174 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 3.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 244 MET cc_start: 0.8608 (tpp) cc_final: 0.8310 (tpp) REVERT: T 19 SER cc_start: 0.8882 (m) cc_final: 0.8439 (p) REVERT: T 49 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7237 (mpp) REVERT: M 156 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8451 (tt) REVERT: M 183 MET cc_start: 0.9266 (ttp) cc_final: 0.8949 (ttm) REVERT: M 229 MET cc_start: 0.8666 (tpp) cc_final: 0.8220 (ttm) REVERT: M 244 MET cc_start: 0.8702 (tpp) cc_final: 0.8435 (tpp) REVERT: M 276 MET cc_start: 0.7760 (mmm) cc_final: 0.7104 (mmt) REVERT: G 19 SER cc_start: 0.8953 (m) cc_final: 0.8509 (p) REVERT: G 30 ASP cc_start: 0.8615 (t0) cc_final: 0.8343 (t0) REVERT: G 48 ARG cc_start: 0.8775 (mmm-85) cc_final: 0.8307 (mmm160) REVERT: G 49 MET cc_start: 0.8513 (mpp) cc_final: 0.7444 (mpp) REVERT: G 56 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7227 (mt) REVERT: I 108 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8420 (pm20) REVERT: I 506 MET cc_start: 0.8858 (tmm) cc_final: 0.8641 (tmm) REVERT: I 777 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8382 (tm-30) outliers start: 23 outliers final: 14 residues processed: 166 average time/residue: 0.4453 time to fit residues: 125.7014 Evaluate side-chains 167 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 356 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Rotamers are restrained with sigma=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: 0.0010 chunk 62 optimal weight: 0.8980 chunk 341 optimal weight: 2.9990 chunk 331 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 333 optimal weight: 5.9990 chunk 379 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 352 optimal weight: 7.9990 overall best weight: 2.7792 ------------------------------------------------------------------------------- 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 ** I 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.068301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.050772 restraints weight = 84306.159| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.32 r_work: 0.2635 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 33870 Z= 0.215 Angle : 0.550 11.839 45972 Z= 0.287 Chirality : 0.044 0.246 4848 Planarity : 0.003 0.046 5976 Dihedral : 4.896 51.769 5014 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 0.83 % Allowed : 8.22 % Favored : 90.94 % 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: 0.18 (0.13), residues: 4118 helix: 1.43 (0.20), residues: 722 sheet: 0.31 (0.14), residues: 1276 loop : -0.41 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.004 0.001 HIS M 71 PHE 0.013 0.001 PHE J 342 TYR 0.019 0.001 TYR T 42 ARG 0.004 0.000 ARG T 95 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01035 ( 16) link_ALPHA2-6 : angle 2.89484 ( 48) hydrogen bonds : bond 0.03571 ( 1420) hydrogen bonds : angle 4.71050 ( 3909) SS BOND : bond 0.00631 ( 2) SS BOND : angle 6.21212 ( 4) glycosidic custom : bond 0.01304 ( 2) glycosidic custom : angle 2.08701 ( 6) covalent geometry : bond 0.00490 (33850) covalent geometry : angle 0.53908 (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 176 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 3.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 244 MET cc_start: 0.8818 (tpp) cc_final: 0.8426 (tpp) REVERT: E 276 MET cc_start: 0.7916 (mmm) cc_final: 0.7303 (mmt) REVERT: T 19 SER cc_start: 0.9002 (m) cc_final: 0.8549 (p) REVERT: T 49 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7321 (mpp) REVERT: T 56 LEU cc_start: 0.7962 (mt) cc_final: 0.7656 (mt) REVERT: M 183 MET cc_start: 0.9281 (ttp) cc_final: 0.8968 (ttm) REVERT: M 216 MET cc_start: 0.7647 (mmt) cc_final: 0.7242 (mmm) REVERT: M 229 MET cc_start: 0.8627 (tpp) cc_final: 0.8188 (ttm) REVERT: G 19 SER cc_start: 0.9029 (m) cc_final: 0.8584 (p) REVERT: G 30 ASP cc_start: 0.8597 (t0) cc_final: 0.8267 (t0) REVERT: G 48 ARG cc_start: 0.8735 (mmm-85) cc_final: 0.8294 (mmm160) REVERT: G 49 MET cc_start: 0.8508 (mpp) cc_final: 0.7427 (mpp) REVERT: G 56 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7507 (mt) REVERT: I 108 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8327 (pm20) REVERT: I 777 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8534 (tm-30) outliers start: 29 outliers final: 21 residues processed: 166 average time/residue: 0.4190 time to fit residues: 118.3907 Evaluate side-chains 168 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 3.513 ------------------------------------------------------------------------------- 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 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 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 109 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 142 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 361 optimal weight: 1.9990 chunk 260 optimal weight: 4.9990 chunk 372 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 360 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 677 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.069773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.052374 restraints weight = 84195.881| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.35 r_work: 0.2671 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33870 Z= 0.128 Angle : 0.513 11.660 45972 Z= 0.268 Chirality : 0.043 0.242 4848 Planarity : 0.003 0.038 5976 Dihedral : 4.731 52.501 5014 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 0.81 % Allowed : 8.28 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.20), residues: 722 sheet: 0.36 (0.15), residues: 1274 loop : -0.37 (0.14), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 486 HIS 0.002 0.001 HIS I 362 PHE 0.010 0.001 PHE J 342 TYR 0.026 0.001 TYR G 42 ARG 0.003 0.000 ARG G 95 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01151 ( 16) link_ALPHA2-6 : angle 2.78631 ( 48) hydrogen bonds : bond 0.03204 ( 1420) hydrogen bonds : angle 4.57828 ( 3909) SS BOND : bond 0.00387 ( 2) SS BOND : angle 6.73698 ( 4) glycosidic custom : bond 0.01389 ( 2) glycosidic custom : angle 2.10678 ( 6) covalent geometry : bond 0.00285 (33850) covalent geometry : angle 0.50131 (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 179 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 3.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 276 MET cc_start: 0.7827 (mmm) cc_final: 0.7250 (mmt) REVERT: T 19 SER cc_start: 0.8972 (m) cc_final: 0.8534 (p) REVERT: T 49 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7273 (mpp) REVERT: T 56 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7473 (mt) REVERT: M 183 MET cc_start: 0.9295 (ttp) cc_final: 0.9012 (ttm) REVERT: M 229 MET cc_start: 0.8718 (tpp) cc_final: 0.8256 (ttm) REVERT: M 244 MET cc_start: 0.8739 (tpp) cc_final: 0.8453 (tpp) REVERT: M 276 MET cc_start: 0.7671 (mmm) cc_final: 0.6998 (mmt) REVERT: G 19 SER cc_start: 0.8955 (m) cc_final: 0.8493 (p) REVERT: G 30 ASP cc_start: 0.8624 (t0) cc_final: 0.8341 (t0) REVERT: G 48 ARG cc_start: 0.8741 (mmm-85) cc_final: 0.8304 (mmm160) REVERT: G 49 MET cc_start: 0.8450 (mpp) cc_final: 0.7375 (mpp) REVERT: G 56 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7102 (mt) REVERT: I 108 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8379 (pm20) REVERT: I 777 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8432 (tm-30) outliers start: 28 outliers final: 20 residues processed: 171 average time/residue: 0.4460 time to fit residues: 130.3311 Evaluate side-chains 173 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 3.738 ------------------------------------------------------------------------------- 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 11 LEU Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 56 LEU 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 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 109 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain J residue 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 574 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 361 optimal weight: 2.9990 chunk 315 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 376 optimal weight: 5.9990 chunk 246 optimal weight: 0.7980 chunk 230 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 107 optimal weight: 0.4980 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 0.9980 chunk 344 optimal weight: 5.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- 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 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.069056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.051329 restraints weight = 84390.903| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.41 r_work: 0.2649 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33870 Z= 0.180 Angle : 0.532 11.948 45972 Z= 0.278 Chirality : 0.044 0.234 4848 Planarity : 0.003 0.037 5976 Dihedral : 4.747 48.358 5014 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.03 % Favored : 95.90 % Rotamer: Outliers : 0.86 % Allowed : 8.28 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.19 (0.13), residues: 4118 helix: 1.43 (0.20), residues: 722 sheet: 0.33 (0.15), residues: 1276 loop : -0.39 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 486 HIS 0.003 0.001 HIS J 343 PHE 0.012 0.001 PHE J 342 TYR 0.024 0.001 TYR G 42 ARG 0.003 0.000 ARG G 95 Details of bonding type rmsd link_ALPHA2-6 : bond 0.01064 ( 16) link_ALPHA2-6 : angle 2.86663 ( 48) hydrogen bonds : bond 0.03395 ( 1420) hydrogen bonds : angle 4.64140 ( 3909) SS BOND : bond 0.00479 ( 2) SS BOND : angle 7.15580 ( 4) glycosidic custom : bond 0.01315 ( 2) glycosidic custom : angle 2.06827 ( 6) covalent geometry : bond 0.00407 (33850) covalent geometry : angle 0.51928 (45914) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16392.69 seconds wall clock time: 287 minutes 7.07 seconds (17227.07 seconds total)