Starting phenix.real_space_refine on Sat Jul 4 11:59:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uja_26562/07_2026/7uja_26562.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uja_26562/07_2026/7uja_26562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7uja_26562/07_2026/7uja_26562.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uja_26562/07_2026/7uja_26562.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uja_26562/07_2026/7uja_26562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uja_26562/07_2026/7uja_26562.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uja_26562/07_2026/7uja_26562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uja_26562/07_2026/7uja_26562.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 13089 2.51 5 N 3471 2.21 5 O 4074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20748 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2859 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 359} Chain: "B" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 934 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "C" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2859 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 359} Chain: "D" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 769 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 91} Chain breaks: 1 Chain: "E" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 940 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "F" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 785 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "G" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 934 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "I" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 940 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "J" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 785 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "K" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2859 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 359} Chain: "L" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 934 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 940 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "O" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 785 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "H" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 769 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 91} Chain breaks: 1 Chain: "M" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 769 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 91} Chain breaks: 1 Chain: "P" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 615 Classifications: {'peptide': 79} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 615 Classifications: {'peptide': 79} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 615 Classifications: {'peptide': 79} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.79, per 1000 atoms: 0.23 Number of scatterers: 20748 At special positions: 0 Unit cell: (156.18, 150.7, 153.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4074 8.00 N 3471 7.00 C 13089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS P 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS P 69 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.29 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.04 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS A 439 " - pdb=" SG CYS P 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS Q 103 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS Q 69 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.04 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 439 " - pdb=" SG CYS Q 37 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.10 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 148 " - pdb=" SG CYS R 103 " distance=2.03 Simple disulfide: pdb=" SG CYS K 212 " - pdb=" SG CYS R 69 " distance=2.03 Simple disulfide: pdb=" SG CYS K 313 " - pdb=" SG CYS K 343 " distance=2.04 Simple disulfide: pdb=" SG CYS K 322 " - pdb=" SG CYS K 333 " distance=2.04 Simple disulfide: pdb=" SG CYS K 358 " - pdb=" SG CYS K 367 " distance=2.04 Simple disulfide: pdb=" SG CYS K 382 " - pdb=" SG CYS K 393 " distance=2.03 Simple disulfide: pdb=" SG CYS K 416 " - pdb=" SG CYS K 422 " distance=2.03 Simple disulfide: pdb=" SG CYS K 439 " - pdb=" SG CYS R 37 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 89 " distance=2.03 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 NAG-ASN " NAG A 601 " - " ASN A 500 " " NAG C 601 " - " ASN C 500 " " NAG K 601 " - " ASN K 500 " Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 1.2 seconds 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4968 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 46 sheets defined 16.6% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 163 through 171 removed outlier: 3.536A pdb=" N ILE A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 removed outlier: 3.538A pdb=" N ILE A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 removed outlier: 3.627A pdb=" N VAL A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 203 through 208' Processing helix chain 'A' and resid 216 through 238 removed outlier: 4.204A pdb=" N VAL A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.631A pdb=" N LEU A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 379 through 385 removed outlier: 3.998A pdb=" N ASN A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.744A pdb=" N PHE A 477 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 506 removed outlier: 3.525A pdb=" N ILE A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.532A pdb=" N HIS B 31 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.045A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.644A pdb=" N LEU C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU C 142 " --> pdb=" O GLY C 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 138 through 142' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 163 through 171 removed outlier: 3.574A pdb=" N ILE C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 200 removed outlier: 3.565A pdb=" N ILE C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.542A pdb=" N VAL C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN C 208 " --> pdb=" O LEU C 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 203 through 208' Processing helix chain 'C' and resid 216 through 227 removed outlier: 4.278A pdb=" N VAL C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 241 removed outlier: 3.570A pdb=" N LEU C 231 " --> pdb=" O ASN C 227 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN C 240 " --> pdb=" O GLU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.609A pdb=" N LEU C 258 " --> pdb=" O ASN C 254 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 368 through 372 removed outlier: 4.088A pdb=" N ASN C 371 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 372 " --> pdb=" O THR C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 372' Processing helix chain 'C' and resid 379 through 385 removed outlier: 4.049A pdb=" N ASN C 383 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 removed outlier: 3.577A pdb=" N PHE C 477 " --> pdb=" O ILE C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 507 removed outlier: 3.678A pdb=" N ILE C 506 " --> pdb=" O SER C 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG C 507 " --> pdb=" O LEU C 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.509A pdb=" N HIS G 31 " --> pdb=" O SER G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.918A pdb=" N THR G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'K' and resid 148 through 159 removed outlier: 4.196A pdb=" N ILE K 152 " --> pdb=" O CYS K 148 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA K 153 " --> pdb=" O ALA K 149 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL K 154 " --> pdb=" O SER K 150 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL K 157 " --> pdb=" O ALA K 153 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU K 158 " --> pdb=" O VAL K 154 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS K 159 " --> pdb=" O SER K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 171 removed outlier: 3.579A pdb=" N ILE K 167 " --> pdb=" O GLU K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 200 removed outlier: 3.588A pdb=" N ILE K 199 " --> pdb=" O LEU K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 208 removed outlier: 3.647A pdb=" N VAL K 207 " --> pdb=" O LEU K 203 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN K 208 " --> pdb=" O LEU K 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 203 through 208' Processing helix chain 'K' and resid 216 through 241 removed outlier: 4.173A pdb=" N VAL K 220 " --> pdb=" O ASN K 216 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU K 222 " --> pdb=" O GLU K 218 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG K 229 " --> pdb=" O GLN K 225 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU K 230 " --> pdb=" O LYS K 226 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU K 231 " --> pdb=" O ASN K 227 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR K 234 " --> pdb=" O LEU K 230 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL K 239 " --> pdb=" O ARG K 235 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 253 through 262 removed outlier: 3.546A pdb=" N LEU K 258 " --> pdb=" O ASN K 254 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER K 259 " --> pdb=" O SER K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 276 removed outlier: 3.566A pdb=" N SER K 276 " --> pdb=" O LYS K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 282 Processing helix chain 'K' and resid 376 through 378 No H-bonds generated for 'chain 'K' and resid 376 through 378' Processing helix chain 'K' and resid 379 through 385 removed outlier: 4.204A pdb=" N ASN K 383 " --> pdb=" O VAL K 379 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE K 384 " --> pdb=" O ASN K 380 " (cutoff:3.500A) Processing helix chain 'K' and resid 473 through 478 removed outlier: 3.913A pdb=" N ASN K 476 " --> pdb=" O PRO K 473 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE K 477 " --> pdb=" O ILE K 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 492 through 507 removed outlier: 3.524A pdb=" N ILE K 506 " --> pdb=" O SER K 502 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG K 507 " --> pdb=" O LEU K 503 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.559A pdb=" N HIS L 31 " --> pdb=" O SER L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.753A pdb=" N THR L 91 " --> pdb=" O PRO L 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'O' and resid 80 through 84 removed outlier: 4.135A pdb=" N PHE O 84 " --> pdb=" O PRO O 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 95 removed outlier: 3.669A pdb=" N LYS P 77 " --> pdb=" O ASP P 73 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE P 79 " --> pdb=" O LYS P 75 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU P 95 " --> pdb=" O THR P 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 97 removed outlier: 3.674A pdb=" N LEU Q 95 " --> pdb=" O THR Q 91 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU Q 96 " --> pdb=" O GLU Q 92 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET Q 97 " --> pdb=" O LEU Q 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 97 removed outlier: 3.505A pdb=" N ILE R 79 " --> pdb=" O LYS R 75 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET R 97 " --> pdb=" O LEU R 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 180 removed outlier: 7.276A pdb=" N SER A 186 " --> pdb=" O THR P 54 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL P 56 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU A 188 " --> pdb=" O VAL P 56 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR P 58 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE A 190 " --> pdb=" O THR P 58 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY P 51 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA A 298 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 214 removed outlier: 3.508A pdb=" N SER A 213 " --> pdb=" O LEU E 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 349 through 352 removed outlier: 3.771A pdb=" N GLY A 340 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER P 38 " --> pdb=" O TYR P 33 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR P 33 " --> pdb=" O SER P 38 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU P 30 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 333 through 336 removed outlier: 3.604A pdb=" N CYS A 333 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 406 through 407 removed outlier: 4.026A pdb=" N CYS A 416 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.546A pdb=" N GLY A 430 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA A 424 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR A 434 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N CYS A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 59 removed outlier: 3.576A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 177 through 180 removed outlier: 7.235A pdb=" N SER C 186 " --> pdb=" O THR Q 54 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL Q 56 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU C 188 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR Q 58 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE C 190 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY Q 51 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA C 298 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 213 through 214 Processing sheet with id=AB2, first strand: chain 'C' and resid 349 through 352 removed outlier: 3.504A pdb=" N CYS C 343 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY C 340 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 316 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER Q 38 " --> pdb=" O TYR Q 33 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR Q 33 " --> pdb=" O SER Q 38 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU Q 30 " --> pdb=" O LYS C 465 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 333 through 336 Processing sheet with id=AB4, first strand: chain 'C' and resid 406 through 407 removed outlier: 4.086A pdb=" N CYS C 416 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 430 through 434 removed outlier: 7.012A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N THR C 434 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N CYS C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.076A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 6 removed outlier: 4.146A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL E 79 " --> pdb=" O CYS E 22 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE E 71 " --> pdb=" O TYR E 80 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU E 82 " --> pdb=" O THR E 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.879A pdb=" N GLU E 10 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.565A pdb=" N THR F 103 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU F 34 " --> pdb=" O PHE F 50 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.565A pdb=" N THR F 103 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR F 98 " --> pdb=" O SER F 91 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AC5, first strand: chain 'G' and resid 45 through 51 removed outlier: 3.668A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.924A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL I 79 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU I 82 " --> pdb=" O THR I 69 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR I 69 " --> pdb=" O GLU I 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 12 removed outlier: 4.010A pdb=" N GLU I 10 " --> pdb=" O LEU I 119 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 107 through 108 Processing sheet with id=AC9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.961A pdb=" N LEU J 34 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 11 Processing sheet with id=AD3, first strand: chain 'K' and resid 177 through 180 removed outlier: 7.120A pdb=" N SER K 186 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL R 56 " --> pdb=" O SER K 186 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU K 188 " --> pdb=" O VAL R 56 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR R 58 " --> pdb=" O LEU K 188 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE K 190 " --> pdb=" O THR R 58 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY R 51 " --> pdb=" O LEU K 305 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA K 298 " --> pdb=" O SER K 290 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 349 through 352 removed outlier: 3.506A pdb=" N CYS K 343 " --> pdb=" O SER K 350 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY K 340 " --> pdb=" O LEU K 316 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU K 316 " --> pdb=" O GLY K 340 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER R 38 " --> pdb=" O TYR R 33 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR R 33 " --> pdb=" O SER R 38 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU R 30 " --> pdb=" O LYS K 465 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 333 through 336 Processing sheet with id=AD6, first strand: chain 'K' and resid 406 through 407 Processing sheet with id=AD7, first strand: chain 'K' and resid 415 through 416 removed outlier: 4.210A pdb=" N CYS K 416 " --> pdb=" O GLY K 438 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 430 through 434 removed outlier: 3.624A pdb=" N ILE K 432 " --> pdb=" O ALA K 424 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA K 424 " --> pdb=" O ILE K 432 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THR K 434 " --> pdb=" O CYS K 422 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N CYS K 422 " --> pdb=" O THR K 434 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AE1, first strand: chain 'L' and resid 58 through 59 removed outlier: 5.440A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 3 through 6 removed outlier: 4.132A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.907A pdb=" N GLU N 10 " --> pdb=" O LEU N 119 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'O' and resid 10 through 11 removed outlier: 6.938A pdb=" N LEU O 34 " --> pdb=" O PHE O 50 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE O 50 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 10 through 11 Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.861A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N HIS H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU H 33 " --> pdb=" O HIS H 49 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'M' and resid 53 through 54 removed outlier: 7.125A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1749 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: 4.51 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6692 1.35 - 1.47: 5065 1.47 - 1.59: 9213 1.59 - 1.72: 0 1.72 - 1.84: 156 Bond restraints: 21126 Sorted by residual: bond pdb=" CA GLN D 90 " pdb=" CB GLN D 90 " ideal model delta sigma weight residual 1.530 1.558 -0.028 1.55e-02 4.16e+03 3.32e+00 bond pdb=" C PRO M 95 " pdb=" N PRO M 96 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.94e+00 bond pdb=" C PRO D 95 " pdb=" N PRO D 96 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.94e+00 bond pdb=" C PRO H 95 " pdb=" N PRO H 96 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.75e+00 bond pdb=" C1 NAG K 601 " pdb=" O5 NAG K 601 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.48e+00 ... (remaining 21121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 28316 2.33 - 4.66: 293 4.66 - 6.98: 34 6.98 - 9.31: 2 9.31 - 11.64: 2 Bond angle restraints: 28647 Sorted by residual: angle pdb=" CA LEU E 29 " pdb=" CB LEU E 29 " pdb=" CG LEU E 29 " ideal model delta sigma weight residual 116.30 127.94 -11.64 3.50e+00 8.16e-02 1.11e+01 angle pdb=" CA GLN D 90 " pdb=" CB GLN D 90 " pdb=" CG GLN D 90 " ideal model delta sigma weight residual 114.10 120.67 -6.57 2.00e+00 2.50e-01 1.08e+01 angle pdb=" C THR I 76 " pdb=" N ASP I 77 " pdb=" CA ASP I 77 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 angle pdb=" CA GLN H 90 " pdb=" CB GLN H 90 " pdb=" CG GLN H 90 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA CYS C 343 " pdb=" CB CYS C 343 " pdb=" SG CYS C 343 " ideal model delta sigma weight residual 114.40 121.20 -6.80 2.30e+00 1.89e-01 8.75e+00 ... (remaining 28642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11259 17.95 - 35.91: 1132 35.91 - 53.86: 260 53.86 - 71.82: 39 71.82 - 89.77: 18 Dihedral angle restraints: 12708 sinusoidal: 4947 harmonic: 7761 Sorted by residual: dihedral pdb=" CB CYS K 148 " pdb=" SG CYS K 148 " pdb=" SG CYS R 103 " pdb=" CB CYS R 103 " ideal model delta sinusoidal sigma weight residual 93.00 156.42 -63.42 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" CB CYS C 148 " pdb=" SG CYS C 148 " pdb=" SG CYS Q 103 " pdb=" CB CYS Q 103 " ideal model delta sinusoidal sigma weight residual 93.00 154.65 -61.65 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CB CYS A 148 " pdb=" SG CYS A 148 " pdb=" SG CYS P 103 " pdb=" CB CYS P 103 " ideal model delta sinusoidal sigma weight residual 93.00 150.95 -57.95 1 1.00e+01 1.00e-02 4.51e+01 ... (remaining 12705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2103 0.031 - 0.062: 790 0.062 - 0.092: 234 0.092 - 0.123: 190 0.123 - 0.154: 13 Chirality restraints: 3330 Sorted by residual: chirality pdb=" CA ASN G 77 " pdb=" N ASN G 77 " pdb=" C ASN G 77 " pdb=" CB ASN G 77 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA VAL L 48 " pdb=" N VAL L 48 " pdb=" C VAL L 48 " pdb=" CB VAL L 48 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA ASP I 77 " pdb=" N ASP I 77 " pdb=" C ASP I 77 " pdb=" CB ASP I 77 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 3327 not shown) Planarity restraints: 3633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 87 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO L 88 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO L 88 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 88 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO H 95 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO H 96 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO H 96 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 96 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO M 95 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO M 96 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO M 96 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO M 96 " -0.026 5.00e-02 4.00e+02 ... (remaining 3630 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 306 2.67 - 3.23: 18828 3.23 - 3.79: 28870 3.79 - 4.34: 39089 4.34 - 4.90: 66770 Nonbonded interactions: 153863 Sorted by model distance: nonbonded pdb=" OD1 ASP J 106 " pdb=" N PHE J 107 " model vdw 2.114 3.120 nonbonded pdb=" O ILE I 110 " pdb=" OG SER K 211 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR K 311 " pdb=" OG SER R 46 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR A 311 " pdb=" OG SER P 46 " model vdw 2.208 3.040 nonbonded pdb=" OG SER A 211 " pdb=" O ILE E 110 " model vdw 2.212 3.040 ... (remaining 153858 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 group one per residue 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.520 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 : 0.003 0.262 21160 Z= 0.152 Angle : 0.674 46.174 28718 Z= 0.345 Chirality : 0.042 0.154 3330 Planarity : 0.004 0.055 3630 Dihedral : 15.003 89.770 7647 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.13 % Allowed : 16.84 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.16), residues: 2652 helix: -1.04 (0.26), residues: 366 sheet: -0.97 (0.19), residues: 816 loop : -2.00 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 85 TYR 0.013 0.001 TYR E 113 PHE 0.015 0.001 PHE E 64 TRP 0.010 0.001 TRP C 314 HIS 0.006 0.001 HIS M 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (21126) covalent geometry : angle 0.58317 / 0.31 (28647) SS BOND : bond 0.04879 / 2.42 ( 31) SS BOND : angle 6.89114 / 2.25 ( 62) hydrogen bonds : bond 0.27510 / 17.98 ( 669) hydrogen bonds : angle 9.56658 / 6.58 ( 1749) link_NAG-ASN : bond 0.00871 / 0.44 ( 3) link_NAG-ASN : angle 6.25396 / 2.91 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 369 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.7301 (tpp) cc_final: 0.7020 (mmm) REVERT: G 83 MET cc_start: 0.6263 (mtm) cc_final: 0.5966 (mtm) REVERT: K 367 CYS cc_start: 0.6300 (m) cc_final: 0.5914 (m) outliers start: 3 outliers final: 2 residues processed: 370 average time/residue: 0.1444 time to fit residues: 84.6442 Evaluate side-chains 331 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 329 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain N residue 28 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 ASN C 284 GLN F 38 GLN G 74 ASN K 227 ASN ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN Q 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.149390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.125745 restraints weight = 30656.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.128419 restraints weight = 19881.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130257 restraints weight = 14620.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.131469 restraints weight = 11780.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131987 restraints weight = 10137.507| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21160 Z= 0.127 Angle : 0.594 10.297 28718 Z= 0.306 Chirality : 0.043 0.155 3330 Planarity : 0.004 0.053 3630 Dihedral : 4.241 31.509 2883 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.58 % Allowed : 17.90 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.16), residues: 2652 helix: 0.08 (0.28), residues: 357 sheet: -0.73 (0.18), residues: 870 loop : -2.04 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 85 TYR 0.016 0.001 TYR B 53 PHE 0.010 0.001 PHE G 68 TRP 0.009 0.001 TRP C 314 HIS 0.004 0.001 HIS M 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (21126) covalent geometry : angle 0.57532 / 0.30 (28647) SS BOND : bond 0.00470 / 0.23 ( 31) SS BOND : angle 1.52814 / 0.84 ( 62) hydrogen bonds : bond 0.04842 / 3.09 ( 669) hydrogen bonds : angle 6.46854 / 4.46 ( 1749) link_NAG-ASN : bond 0.00642 / 0.32 ( 3) link_NAG-ASN : angle 7.42467 / 3.46 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 340 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.8829 (mmm) cc_final: 0.8564 (mtt) REVERT: C 396 MET cc_start: 0.7832 (ptm) cc_final: 0.7606 (ptp) REVERT: D 90 GLN cc_start: 0.8129 (pp30) cc_final: 0.7789 (pp30) REVERT: F 103 THR cc_start: 0.9015 (t) cc_final: 0.8620 (m) REVERT: K 236 GLU cc_start: 0.6925 (tt0) cc_final: 0.6705 (tt0) REVERT: O 103 THR cc_start: 0.8828 (t) cc_final: 0.8576 (m) REVERT: M 90 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8041 (pp30) outliers start: 84 outliers final: 50 residues processed: 395 average time/residue: 0.1354 time to fit residues: 85.9821 Evaluate side-chains 368 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 317 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain G residue 84 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 53 SER Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 99 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 0.0770 chunk 246 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 201 optimal weight: 9.9990 chunk 164 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 256 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 ASN C 284 GLN I 6 GLN J 38 GLN K 227 ASN K 284 GLN L 82 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.150611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127216 restraints weight = 30595.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129848 restraints weight = 19674.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.131420 restraints weight = 14414.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132830 restraints weight = 11752.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.133551 restraints weight = 10062.273| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21160 Z= 0.110 Angle : 0.570 11.044 28718 Z= 0.293 Chirality : 0.043 0.160 3330 Planarity : 0.004 0.054 3630 Dihedral : 4.086 31.613 2881 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.31 % Allowed : 18.03 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.16), residues: 2652 helix: 0.48 (0.29), residues: 357 sheet: -0.79 (0.18), residues: 894 loop : -1.94 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 85 TYR 0.014 0.001 TYR C 417 PHE 0.010 0.001 PHE I 59 TRP 0.009 0.001 TRP C 314 HIS 0.006 0.001 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (21126) covalent geometry : angle 0.55395 / 0.29 (28647) SS BOND : bond 0.00357 / 0.19 ( 31) SS BOND : angle 1.33819 / 0.73 ( 62) hydrogen bonds : bond 0.03720 / 2.38 ( 669) hydrogen bonds : angle 5.79254 / 3.99 ( 1749) link_NAG-ASN : bond 0.00675 / 0.34 ( 3) link_NAG-ASN : angle 7.01565 / 3.29 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 343 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 396 MET cc_start: 0.7923 (ptm) cc_final: 0.7717 (ptp) REVERT: D 90 GLN cc_start: 0.8249 (pp30) cc_final: 0.7660 (pp30) REVERT: H 50 ASP cc_start: 0.8380 (m-30) cc_final: 0.8001 (m-30) REVERT: H 90 GLN cc_start: 0.7996 (pp30) cc_final: 0.7668 (pp30) REVERT: M 50 ASP cc_start: 0.8660 (m-30) cc_final: 0.8066 (m-30) outliers start: 101 outliers final: 63 residues processed: 412 average time/residue: 0.1327 time to fit residues: 87.6037 Evaluate side-chains 382 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 319 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain G residue 84 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 106 ASP Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain R residue 29 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 185 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 253 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 ASN C 284 GLN F 6 GLN K 284 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.149275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126407 restraints weight = 30762.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.127935 restraints weight = 23447.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.129123 restraints weight = 18278.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129367 restraints weight = 15456.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129658 restraints weight = 13932.466| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21160 Z= 0.128 Angle : 0.578 11.227 28718 Z= 0.295 Chirality : 0.043 0.162 3330 Planarity : 0.004 0.056 3630 Dihedral : 4.118 31.825 2881 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 5.07 % Allowed : 18.37 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.16), residues: 2652 helix: 0.25 (0.28), residues: 375 sheet: -0.83 (0.18), residues: 924 loop : -1.98 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 85 TYR 0.017 0.001 TYR C 342 PHE 0.009 0.001 PHE A 237 TRP 0.011 0.001 TRP C 314 HIS 0.007 0.002 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (21126) covalent geometry : angle 0.56310 / 0.29 (28647) SS BOND : bond 0.00412 / 0.25 ( 31) SS BOND : angle 1.42822 / 0.78 ( 62) hydrogen bonds : bond 0.03508 / 2.23 ( 669) hydrogen bonds : angle 5.53621 / 3.82 ( 1749) link_NAG-ASN : bond 0.00566 / 0.28 ( 3) link_NAG-ASN : angle 6.57924 / 3.09 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 334 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.8813 (mmm) cc_final: 0.8524 (mtt) REVERT: A 289 MET cc_start: 0.7404 (mmm) cc_final: 0.7129 (mmm) REVERT: B 54 ASP cc_start: 0.7405 (p0) cc_final: 0.6827 (p0) REVERT: C 396 MET cc_start: 0.7724 (ptm) cc_final: 0.7508 (ptp) REVERT: D 82 ASP cc_start: 0.7595 (m-30) cc_final: 0.7340 (m-30) REVERT: D 90 GLN cc_start: 0.8419 (pp30) cc_final: 0.7766 (pp30) REVERT: E 52 GLU cc_start: 0.7434 (mp0) cc_final: 0.7007 (mp0) REVERT: K 289 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6681 (tmm) REVERT: L 58 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8318 (p) REVERT: H 65 ARG cc_start: 0.8043 (ttm110) cc_final: 0.7637 (ttp-110) REVERT: H 90 GLN cc_start: 0.8075 (pp30) cc_final: 0.7647 (pp30) outliers start: 119 outliers final: 91 residues processed: 417 average time/residue: 0.1342 time to fit residues: 89.6908 Evaluate side-chains 416 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 323 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain G residue 84 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 289 MET Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 349 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 396 MET Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 53 SER Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 ASP Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 24 GLN Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 95 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 143 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 148 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 ASN F 38 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.148906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125285 restraints weight = 30527.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128003 restraints weight = 19379.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129880 restraints weight = 14108.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131118 restraints weight = 11298.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.131660 restraints weight = 9698.326| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21160 Z= 0.134 Angle : 0.581 9.636 28718 Z= 0.297 Chirality : 0.043 0.163 3330 Planarity : 0.004 0.058 3630 Dihedral : 4.154 32.020 2881 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.58 % Allowed : 18.63 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.16), residues: 2652 helix: 0.29 (0.28), residues: 375 sheet: -0.77 (0.18), residues: 903 loop : -2.00 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 85 TYR 0.021 0.001 TYR G 59 PHE 0.010 0.001 PHE D 71 TRP 0.010 0.001 TRP C 314 HIS 0.008 0.002 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (21126) covalent geometry : angle 0.56660 / 0.29 (28647) SS BOND : bond 0.00370 / 0.19 ( 31) SS BOND : angle 1.44798 / 0.77 ( 62) hydrogen bonds : bond 0.03429 / 2.18 ( 669) hydrogen bonds : angle 5.43257 / 3.75 ( 1749) link_NAG-ASN : bond 0.00536 / 0.27 ( 3) link_NAG-ASN : angle 6.28647 / 2.95 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 333 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.8792 (mmm) cc_final: 0.8555 (mtt) REVERT: B 77 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7750 (p0) REVERT: C 396 MET cc_start: 0.7730 (ptm) cc_final: 0.7503 (ptp) REVERT: D 90 GLN cc_start: 0.8544 (pp30) cc_final: 0.7881 (pp30) REVERT: E 6 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7603 (mm110) REVERT: F 79 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.5927 (tt) REVERT: G 56 GLU cc_start: 0.8152 (mp0) cc_final: 0.7767 (mp0) REVERT: K 289 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6895 (tmm) REVERT: K 367 CYS cc_start: 0.5925 (m) cc_final: 0.5492 (m) REVERT: L 58 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8425 (p) REVERT: H 73 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7959 (tt) REVERT: H 90 GLN cc_start: 0.8155 (pp30) cc_final: 0.7644 (pp30) REVERT: M 50 ASP cc_start: 0.8818 (m-30) cc_final: 0.8133 (m-30) REVERT: M 55 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6978 (mm-30) REVERT: R 49 ARG cc_start: 0.7657 (tmm160) cc_final: 0.7418 (tmm160) outliers start: 131 outliers final: 102 residues processed: 422 average time/residue: 0.1368 time to fit residues: 92.6079 Evaluate side-chains 428 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 321 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain G residue 84 ASN Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 289 MET Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 349 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 396 MET Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 27 HIS Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 ASP Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 95 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 182 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 254 optimal weight: 0.9990 chunk 256 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 197 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 ASN C 284 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.150211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128005 restraints weight = 30467.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129747 restraints weight = 19630.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.130900 restraints weight = 14243.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.131560 restraints weight = 13216.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.131668 restraints weight = 11055.400| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21160 Z= 0.112 Angle : 0.575 10.956 28718 Z= 0.291 Chirality : 0.043 0.161 3330 Planarity : 0.004 0.057 3630 Dihedral : 4.074 32.009 2881 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 5.63 % Allowed : 18.93 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.16), residues: 2652 helix: 0.68 (0.29), residues: 360 sheet: -0.71 (0.18), residues: 903 loop : -1.92 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 85 TYR 0.022 0.001 TYR A 342 PHE 0.009 0.001 PHE D 71 TRP 0.011 0.001 TRP C 314 HIS 0.009 0.001 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (21126) covalent geometry : angle 0.56148 / 0.29 (28647) SS BOND : bond 0.00377 / 0.21 ( 31) SS BOND : angle 1.44472 / 0.77 ( 62) hydrogen bonds : bond 0.03187 / 2.03 ( 669) hydrogen bonds : angle 5.27469 / 3.64 ( 1749) link_NAG-ASN : bond 0.00543 / 0.27 ( 3) link_NAG-ASN : angle 6.00676 / 2.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 348 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 TYR cc_start: 0.8754 (m-80) cc_final: 0.8468 (m-80) REVERT: B 77 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7761 (p0) REVERT: C 396 MET cc_start: 0.7742 (ptm) cc_final: 0.7499 (ptp) REVERT: D 90 GLN cc_start: 0.8557 (pp30) cc_final: 0.7865 (pp30) REVERT: E 6 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7740 (mm110) REVERT: F 79 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5912 (tt) REVERT: K 289 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6689 (tmm) REVERT: K 367 CYS cc_start: 0.5902 (m) cc_final: 0.5509 (m) REVERT: L 58 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8411 (p) REVERT: H 65 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7641 (ttp-110) REVERT: H 73 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7935 (tt) REVERT: H 90 GLN cc_start: 0.8207 (pp30) cc_final: 0.7625 (pp30) REVERT: M 7 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8135 (m) REVERT: M 50 ASP cc_start: 0.8732 (m-30) cc_final: 0.8096 (m-30) outliers start: 132 outliers final: 103 residues processed: 438 average time/residue: 0.1407 time to fit residues: 98.7459 Evaluate side-chains 443 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 334 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain G residue 84 ASN Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 289 MET Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 349 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 396 MET Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 ASP Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 95 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 247 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 ASN C 183 ASN C 208 ASN C 284 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.145680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122541 restraints weight = 30820.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.124170 restraints weight = 24014.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.125408 restraints weight = 18740.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125847 restraints weight = 15215.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.126039 restraints weight = 13836.353| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21160 Z= 0.216 Angle : 0.659 9.897 28718 Z= 0.337 Chirality : 0.046 0.194 3330 Planarity : 0.004 0.057 3630 Dihedral : 4.462 32.342 2881 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 5.67 % Allowed : 20.33 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.16), residues: 2652 helix: 0.06 (0.28), residues: 378 sheet: -0.76 (0.18), residues: 882 loop : -2.11 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 282 TYR 0.026 0.002 TYR R 86 PHE 0.014 0.002 PHE E 95 TRP 0.013 0.001 TRP C 314 HIS 0.010 0.002 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (21126) covalent geometry : angle 0.64585 / 0.33 (28647) SS BOND : bond 0.00442 / 0.24 ( 31) SS BOND : angle 1.85376 / 0.97 ( 62) hydrogen bonds : bond 0.03916 / 2.48 ( 669) hydrogen bonds : angle 5.60520 / 3.88 ( 1749) link_NAG-ASN : bond 0.00418 / 0.21 ( 3) link_NAG-ASN : angle 5.98586 / 2.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 325 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7880 (t80) REVERT: B 77 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.7903 (p0) REVERT: D 90 GLN cc_start: 0.8628 (pp30) cc_final: 0.8022 (pp30) REVERT: E 6 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7595 (mm110) REVERT: F 79 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6526 (tt) REVERT: L 58 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8188 (p) REVERT: H 73 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7907 (tt) REVERT: H 90 GLN cc_start: 0.8344 (pp30) cc_final: 0.7771 (pp30) outliers start: 133 outliers final: 107 residues processed: 419 average time/residue: 0.1300 time to fit residues: 88.1999 Evaluate side-chains 426 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 314 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain G residue 84 ASN Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 349 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 396 MET Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 ASP Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 64 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 113 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 172 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 167 optimal weight: 0.6980 chunk 212 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 ASN C 284 GLN F 38 GLN I 6 GLN O 6 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129856 restraints weight = 30150.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.132530 restraints weight = 19167.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134370 restraints weight = 14110.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.135676 restraints weight = 11413.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136386 restraints weight = 9784.613| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21160 Z= 0.112 Angle : 0.600 9.231 28718 Z= 0.305 Chirality : 0.043 0.165 3330 Planarity : 0.004 0.055 3630 Dihedral : 4.205 31.831 2881 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.99 % Allowed : 21.18 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.16), residues: 2652 helix: 0.65 (0.29), residues: 351 sheet: -0.74 (0.18), residues: 903 loop : -1.89 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 85 TYR 0.022 0.001 TYR G 59 PHE 0.017 0.001 PHE E 59 TRP 0.011 0.001 TRP K 314 HIS 0.009 0.001 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (21126) covalent geometry : angle 0.58737 / 0.30 (28647) SS BOND : bond 0.00442 / 0.22 ( 31) SS BOND : angle 1.50622 / 0.85 ( 62) hydrogen bonds : bond 0.03128 / 1.99 ( 669) hydrogen bonds : angle 5.24284 / 3.62 ( 1749) link_NAG-ASN : bond 0.00509 / 0.26 ( 3) link_NAG-ASN : angle 5.75026 / 2.71 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 334 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 TYR cc_start: 0.8661 (m-80) cc_final: 0.8091 (m-80) REVERT: B 32 TYR cc_start: 0.8698 (m-80) cc_final: 0.8376 (m-80) REVERT: B 77 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7872 (p0) REVERT: D 90 GLN cc_start: 0.8607 (pp30) cc_final: 0.8064 (pp30) REVERT: E 6 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7565 (mm110) REVERT: F 79 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6106 (tt) REVERT: K 289 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6881 (tmm) REVERT: K 367 CYS cc_start: 0.6234 (m) cc_final: 0.5865 (m) REVERT: L 58 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8313 (p) REVERT: H 65 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7581 (ttp-110) REVERT: H 73 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7881 (tt) REVERT: H 90 GLN cc_start: 0.8306 (pp30) cc_final: 0.7712 (pp30) REVERT: M 50 ASP cc_start: 0.8692 (m-30) cc_final: 0.7987 (m-30) outliers start: 117 outliers final: 91 residues processed: 414 average time/residue: 0.1332 time to fit residues: 88.4592 Evaluate side-chains 421 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 325 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain G residue 84 ASN Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 289 MET Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 349 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 396 MET Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 27 HIS Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 61 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 233 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 255 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 chunk 227 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 192 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS C 284 GLN G 84 ASN K 183 ASN O 6 GLN M 49 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120556 restraints weight = 30899.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121543 restraints weight = 24391.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122300 restraints weight = 20457.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123341 restraints weight = 17130.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123569 restraints weight = 14686.706| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 21160 Z= 0.272 Angle : 0.729 10.833 28718 Z= 0.374 Chirality : 0.048 0.203 3330 Planarity : 0.005 0.074 3630 Dihedral : 4.794 32.222 2881 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 5.20 % Allowed : 21.14 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.16), residues: 2652 helix: -0.14 (0.27), residues: 378 sheet: -0.86 (0.18), residues: 885 loop : -2.19 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 85 TYR 0.032 0.002 TYR R 86 PHE 0.016 0.002 PHE E 95 TRP 0.015 0.002 TRP C 314 HIS 0.010 0.002 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.27 (21126) covalent geometry : angle 0.71410 / 0.37 (28647) SS BOND : bond 0.00543 / 0.27 ( 31) SS BOND : angle 2.29416 / 1.29 ( 62) hydrogen bonds : bond 0.04366 / 2.76 ( 669) hydrogen bonds : angle 5.85365 / 4.06 ( 1749) link_NAG-ASN : bond 0.00298 / 0.15 ( 3) link_NAG-ASN : angle 5.93439 / 2.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 318 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7725 (t80) REVERT: B 77 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.8088 (p0) REVERT: C 265 PRO cc_start: 0.8918 (Cg_exo) cc_final: 0.8659 (Cg_endo) REVERT: D 90 GLN cc_start: 0.8608 (pp30) cc_final: 0.8013 (pp30) REVERT: E 6 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7635 (mm110) REVERT: F 79 LEU cc_start: 0.6920 (tt) cc_final: 0.6682 (tt) REVERT: K 410 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8527 (mt) REVERT: O 17 GLU cc_start: 0.7496 (tt0) cc_final: 0.7237 (tt0) REVERT: H 33 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8520 (mm) REVERT: H 65 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7739 (ttp-110) REVERT: H 73 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7860 (tt) REVERT: H 90 GLN cc_start: 0.8372 (pp30) cc_final: 0.7781 (pp30) REVERT: M 39 LYS cc_start: 0.7458 (mtmt) cc_final: 0.7016 (mtmt) outliers start: 122 outliers final: 104 residues processed: 403 average time/residue: 0.1320 time to fit residues: 86.1577 Evaluate side-chains 422 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 313 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 349 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 396 MET Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain K residue 410 LEU Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain O residue 106 ASP Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 25 optimal weight: 0.5980 chunk 158 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 8 optimal weight: 0.0270 chunk 145 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 244 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS K 284 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.153334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.129665 restraints weight = 30236.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.132424 restraints weight = 19522.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.134316 restraints weight = 14320.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.135494 restraints weight = 11534.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136377 restraints weight = 9971.189| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21160 Z= 0.111 Angle : 0.623 11.758 28718 Z= 0.316 Chirality : 0.044 0.237 3330 Planarity : 0.004 0.064 3630 Dihedral : 4.327 32.002 2881 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.05 % Allowed : 22.55 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.16), residues: 2652 helix: 0.63 (0.29), residues: 351 sheet: -0.78 (0.18), residues: 903 loop : -1.92 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 85 TYR 0.021 0.001 TYR G 59 PHE 0.014 0.001 PHE E 59 TRP 0.012 0.001 TRP K 314 HIS 0.008 0.001 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (21126) covalent geometry : angle 0.61192 / 0.31 (28647) SS BOND : bond 0.00469 / 0.25 ( 31) SS BOND : angle 1.50707 / 0.83 ( 62) hydrogen bonds : bond 0.03135 / 1.99 ( 669) hydrogen bonds : angle 5.28086 / 3.66 ( 1749) link_NAG-ASN : bond 0.00521 / 0.26 ( 3) link_NAG-ASN : angle 5.69891 / 2.69 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5304 Ramachandran restraints generated. 2652 Oldfield, 0 Emsley, 2652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 329 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 TYR cc_start: 0.8670 (m-80) cc_final: 0.8099 (m-80) REVERT: A 367 CYS cc_start: 0.6322 (m) cc_final: 0.5951 (m) REVERT: B 77 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.8036 (p0) REVERT: D 90 GLN cc_start: 0.8448 (pp30) cc_final: 0.7866 (pp30) REVERT: E 6 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7595 (mm110) REVERT: K 289 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6916 (tmm) REVERT: K 410 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8329 (mt) REVERT: L 58 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8298 (p) REVERT: H 65 ARG cc_start: 0.8034 (ttm110) cc_final: 0.7583 (ttp-110) REVERT: H 73 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7857 (tt) REVERT: H 90 GLN cc_start: 0.8433 (pp30) cc_final: 0.7855 (pp30) REVERT: M 50 ASP cc_start: 0.8599 (m-30) cc_final: 0.7993 (m-30) REVERT: R 49 ARG cc_start: 0.7685 (tmm160) cc_final: 0.7433 (tmm160) outliers start: 95 outliers final: 81 residues processed: 395 average time/residue: 0.1330 time to fit residues: 84.1772 Evaluate side-chains 416 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 330 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 289 MET Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 335 THR Chi-restraints excluded: chain K residue 349 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 396 MET Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain K residue 410 LEU Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 20 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 77 ASN Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 96 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 111 optimal weight: 0.0070 chunk 6 optimal weight: 0.9980 chunk 229 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 214 optimal weight: 0.8980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.150087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.126665 restraints weight = 30562.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129312 restraints weight = 19636.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131174 restraints weight = 14402.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.132332 restraints weight = 11558.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.133178 restraints weight = 9933.333| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21160 Z= 0.114 Angle : 0.615 11.449 28718 Z= 0.310 Chirality : 0.043 0.196 3330 Planarity : 0.004 0.063 3630 Dihedral : 4.172 31.947 2881 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.88 % Allowed : 22.85 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.16), residues: 2652 helix: 0.77 (0.29), residues: 360 sheet: -0.70 (0.18), residues: 903 loop : -1.87 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 85 TYR 0.020 0.001 TYR G 59 PHE 0.011 0.001 PHE D 71 TRP 0.008 0.001 TRP K 314 HIS 0.009 0.001 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (21126) covalent geometry : angle 0.60401 / 0.31 (28647) SS BOND : bond 0.00402 / 0.21 ( 31) SS BOND : angle 1.45749 / 0.81 ( 62) hydrogen bonds : bond 0.03072 / 1.95 ( 669) hydrogen bonds : angle 5.14133 / 3.55 ( 1749) link_NAG-ASN : bond 0.00496 / 0.25 ( 3) link_NAG-ASN : angle 5.49937 / 2.60 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3403.35 seconds wall clock time: 59 minutes 49.47 seconds (3589.47 seconds total)