Starting phenix.real_space_refine on Sun Aug 24 14:44:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uja_26562/08_2025/7uja_26562.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uja_26562/08_2025/7uja_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 { model { file = "/net/cci-nas-00/data/ceres_data/7uja_26562/08_2025/7uja_26562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uja_26562/08_2025/7uja_26562.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uja_26562/08_2025/7uja_26562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uja_26562/08_2025/7uja_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-2.0-5787/lib/python3.9/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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.11, per 1000 atoms: 0.25 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: 1.68 Conformation dependent library (CDL) restraints added in 918.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.97 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: 4.18 Time building geometry restraints manager: 2.28 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: 11310 17.95 - 35.91: 1132 35.91 - 53.86: 268 53.86 - 71.82: 43 71.82 - 89.77: 18 Dihedral angle restraints: 12771 sinusoidal: 5010 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 12768 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: 1.520 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.390 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 15.085 89.770 7710 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 aren 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 covalent geometry : bond 0.00256 (21126) covalent geometry : angle 0.58317 (28647) SS BOND : bond 0.04879 ( 31) SS BOND : angle 6.89114 ( 62) hydrogen bonds : bond 0.27510 ( 669) hydrogen bonds : angle 9.56658 ( 1749) link_NAG-ASN : bond 0.00871 ( 3) link_NAG-ASN : angle 6.25396 ( 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 : 0.842 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: 0.1489 time to fit residues: 86.8929 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 : 0.873 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 183 ASN C 284 GLN F 38 GLN G 74 ASN K 227 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.149363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125873 restraints weight = 30663.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128499 restraints weight = 19751.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.130335 restraints weight = 14534.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131541 restraints weight = 11682.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132190 restraints weight = 10062.645| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1046 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= 0.128 Angle : 0.596 10.259 28718 Z= 0.309 Chirality : 0.043 0.156 3330 Planarity : 0.004 0.055 3630 Dihedral : 4.813 40.920 2946 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.58 % Allowed : 17.65 % Favored : 78.77 % 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 aren not related in a simple way. whole: -1.99 (0.16), residues: 2652 helix: -0.20 (0.28), residues: 375 sheet: -0.73 (0.18), residues: 870 loop : -2.06 (0.15), residues: 1407 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 0.005 0.001 HIS M 37 Details of bonding type rmsd covalent geometry : bond 0.00290 (21126) covalent geometry : angle 0.57772 (28647) SS BOND : bond 0.00452 ( 31) SS BOND : angle 1.52054 ( 62) hydrogen bonds : bond 0.04696 ( 669) hydrogen bonds : angle 6.48120 ( 1749) link_NAG-ASN : bond 0.00632 ( 3) link_NAG-ASN : angle 7.55000 ( 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 422 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 338 time to evaluate : 0.835 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: 0.8828 (mmm) cc_final: 0.8587 (mtt) REVERT: C 396 MET cc_start: 0.7814 (ptm) cc_final: 0.7586 (ptp) REVERT: D 90 GLN cc_start: 0.8128 (pp30) cc_final: 0.7780 (pp30) REVERT: F 103 THR cc_start: 0.9014 (t) cc_final: 0.8619 (m) REVERT: K 236 GLU cc_start: 0.6926 (tt0) cc_final: 0.6702 (tt0) REVERT: O 103 THR cc_start: 0.8827 (t) cc_final: 0.8572 (m) REVERT: M 90 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.8038 (pp30) outliers start: 84 outliers final: 50 residues processed: 393 average time/residue: 0.1399 time to fit residues: 88.1512 Evaluate side-chains 364 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 313 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 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 91 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: 6.9990 chunk 246 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 201 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 256 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN I 6 GLN 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.148486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.126472 restraints weight = 30673.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127005 restraints weight = 21071.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.127925 restraints weight = 17303.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.128661 restraints weight = 14317.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.128802 restraints weight = 13266.065| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1297 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= 0.138 Angle : 0.591 11.021 28718 Z= 0.304 Chirality : 0.043 0.162 3330 Planarity : 0.004 0.055 3630 Dihedral : 4.705 40.713 2944 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.94 % Allowed : 17.65 % Favored : 77.41 % 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 aren not related in a simple way. whole: -1.95 (0.16), residues: 2652 helix: 0.04 (0.28), residues: 375 sheet: -0.84 (0.18), residues: 894 loop : -2.01 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 85 TYR 0.018 0.001 TYR P 86 PHE 0.010 0.001 PHE G 68 TRP 0.010 0.001 TRP C 314 HIS 0.006 0.002 HIS I 66 Details of bonding type rmsd covalent geometry : bond 0.00326 (21126) covalent geometry : angle 0.57425 (28647) SS BOND : bond 0.00327 ( 31) SS BOND : angle 1.51322 ( 62) hydrogen bonds : bond 0.03967 ( 669) hydrogen bonds : angle 5.89216 ( 1749) link_NAG-ASN : bond 0.00542 ( 3) link_NAG-ASN : angle 7.11034 ( 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 445 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 329 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ASP cc_start: 0.7277 (p0) cc_final: 0.6763 (p0) REVERT: C 396 MET cc_start: 0.7846 (ptm) cc_final: 0.7638 (ptp) REVERT: D 90 GLN cc_start: 0.8344 (pp30) cc_final: 0.7768 (pp30) REVERT: L 32 TYR cc_start: 0.8668 (m-80) cc_final: 0.8455 (m-80) REVERT: O 103 THR cc_start: 0.8818 (t) cc_final: 0.8608 (m) REVERT: M 50 ASP cc_start: 0.8840 (m-30) cc_final: 0.8169 (m-30) outliers start: 116 outliers final: 80 residues processed: 413 average time/residue: 0.1392 time to fit residues: 92.0165 Evaluate side-chains 396 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 316 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 A residue 482 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 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 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 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 164 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 300 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 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 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 96 ILE 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 64 ILE 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 Q residue 100 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 95 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 185 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 253 optimal weight: 0.6980 chunk 102 optimal weight: 0.0570 chunk 134 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 219 optimal weight: 10.0000 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN C 284 GLN F 6 GLN F 38 GLN J 38 GLN L 82 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.150803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127559 restraints weight = 30705.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130232 restraints weight = 19598.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132080 restraints weight = 14301.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.133276 restraints weight = 11463.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.134153 restraints weight = 9864.143| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21160 Z= 0.104 Angle : 0.568 9.248 28718 Z= 0.289 Chirality : 0.043 0.160 3330 Planarity : 0.004 0.055 3630 Dihedral : 4.460 39.316 2944 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 4.60 % Allowed : 18.93 % Favored : 76.47 % 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 aren not related in a simple way. whole: -1.75 (0.16), residues: 2652 helix: 0.61 (0.29), residues: 357 sheet: -0.84 (0.18), residues: 930 loop : -1.89 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 85 TYR 0.021 0.001 TYR A 342 PHE 0.009 0.001 PHE K 237 TRP 0.012 0.001 TRP C 314 HIS 0.006 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00239 (21126) covalent geometry : angle 0.55306 (28647) SS BOND : bond 0.00415 ( 31) SS BOND : angle 1.25536 ( 62) hydrogen bonds : bond 0.03284 ( 669) hydrogen bonds : angle 5.44883 ( 1749) link_NAG-ASN : bond 0.00533 ( 3) link_NAG-ASN : angle 6.63496 ( 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: 108 poor density : 345 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.7360 (mmm) cc_final: 0.7094 (mmm) REVERT: C 396 MET cc_start: 0.7735 (ptm) cc_final: 0.7495 (ptp) REVERT: D 82 ASP cc_start: 0.7690 (m-30) cc_final: 0.7448 (m-30) REVERT: D 90 GLN cc_start: 0.8318 (pp30) cc_final: 0.7653 (pp30) REVERT: E 52 GLU cc_start: 0.7549 (mp0) cc_final: 0.7207 (mp0) REVERT: J 10 THR cc_start: 0.7807 (m) cc_final: 0.7591 (p) REVERT: K 289 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6674 (tmm) REVERT: H 50 ASP cc_start: 0.8329 (m-30) cc_final: 0.8008 (m-30) REVERT: H 65 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7604 (ttp-110) REVERT: H 73 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7813 (tt) REVERT: M 50 ASP cc_start: 0.8594 (m-30) cc_final: 0.8134 (m-30) outliers start: 108 outliers final: 77 residues processed: 417 average time/residue: 0.1420 time to fit residues: 93.9634 Evaluate side-chains 399 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 320 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 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 29 ILE 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 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 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 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 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 349 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 398 SER 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 34 ILE Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS 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 53 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 29 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 73 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 P residue 29 THR 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 R residue 29 THR Chi-restraints excluded: chain R residue 64 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 143 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 254 optimal weight: 0.0030 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN C 284 GLN D 89 GLN O 6 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.150425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127049 restraints weight = 30465.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129716 restraints weight = 19510.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.131523 restraints weight = 14249.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.132816 restraints weight = 11408.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.133530 restraints weight = 9793.080| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1633 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= 0.113 Angle : 0.570 11.147 28718 Z= 0.290 Chirality : 0.043 0.161 3330 Planarity : 0.004 0.056 3630 Dihedral : 4.423 39.601 2944 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.29 % Allowed : 18.20 % Favored : 76.51 % 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 aren not related in a simple way. whole: -1.70 (0.16), residues: 2652 helix: 0.66 (0.29), residues: 360 sheet: -0.71 (0.18), residues: 903 loop : -1.94 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 85 TYR 0.017 0.001 TYR A 342 PHE 0.010 0.001 PHE D 71 TRP 0.008 0.001 TRP C 314 HIS 0.008 0.001 HIS I 66 Details of bonding type rmsd covalent geometry : bond 0.00264 (21126) covalent geometry : angle 0.55610 (28647) SS BOND : bond 0.00346 ( 31) SS BOND : angle 1.32295 ( 62) hydrogen bonds : bond 0.03221 ( 669) hydrogen bonds : angle 5.29641 ( 1749) link_NAG-ASN : bond 0.00494 ( 3) link_NAG-ASN : angle 6.28721 ( 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 460 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 336 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.7181 (mmm) cc_final: 0.6953 (mmm) REVERT: B 77 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7713 (p0) REVERT: C 396 MET cc_start: 0.7729 (ptm) cc_final: 0.7478 (ptp) REVERT: C 398 SER cc_start: 0.8161 (m) cc_final: 0.7847 (t) REVERT: D 82 ASP cc_start: 0.7895 (m-30) cc_final: 0.7658 (m-30) REVERT: D 90 GLN cc_start: 0.8458 (pp30) cc_final: 0.7787 (pp30) REVERT: E 52 GLU cc_start: 0.7568 (mp0) cc_final: 0.7188 (mp0) REVERT: G 56 GLU cc_start: 0.8181 (mp0) cc_final: 0.7784 (mp0) REVERT: K 367 CYS cc_start: 0.5880 (m) cc_final: 0.5466 (m) REVERT: H 50 ASP cc_start: 0.8344 (m-30) cc_final: 0.8015 (m-30) outliers start: 124 outliers final: 92 residues processed: 423 average time/residue: 0.1421 time to fit residues: 95.6103 Evaluate side-chains 415 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 322 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 68 LEU Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS 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 76 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 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 100 THR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 64 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 182 optimal weight: 0.5980 chunk 69 optimal weight: 0.3980 chunk 60 optimal weight: 0.0980 chunk 254 optimal weight: 1.9990 chunk 256 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 172 optimal weight: 0.2980 chunk 248 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 197 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN C 284 GLN K 284 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.130050 restraints weight = 30353.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132712 restraints weight = 19175.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134439 restraints weight = 13992.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.135782 restraints weight = 11288.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.136514 restraints weight = 9662.381| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21160 Z= 0.095 Angle : 0.558 9.602 28718 Z= 0.282 Chirality : 0.042 0.161 3330 Planarity : 0.004 0.058 3630 Dihedral : 4.221 36.925 2944 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.60 % Allowed : 19.14 % Favored : 76.26 % 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 aren not related in a simple way. whole: -1.57 (0.16), residues: 2652 helix: 0.77 (0.29), residues: 366 sheet: -0.58 (0.18), residues: 894 loop : -1.90 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 85 TYR 0.017 0.001 TYR C 342 PHE 0.008 0.001 PHE L 29 TRP 0.008 0.001 TRP B 47 HIS 0.008 0.001 HIS I 66 Details of bonding type rmsd covalent geometry : bond 0.00213 (21126) covalent geometry : angle 0.54598 (28647) SS BOND : bond 0.00338 ( 31) SS BOND : angle 1.19423 ( 62) hydrogen bonds : bond 0.02863 ( 669) hydrogen bonds : angle 5.00137 ( 1749) link_NAG-ASN : bond 0.00484 ( 3) link_NAG-ASN : angle 5.89834 ( 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 448 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 340 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7676 (p0) REVERT: C 396 MET cc_start: 0.7751 (ptm) cc_final: 0.7470 (ptp) REVERT: C 398 SER cc_start: 0.8061 (m) cc_final: 0.7736 (t) REVERT: D 23 CYS cc_start: 0.7832 (t) cc_final: 0.6616 (p) REVERT: D 90 GLN cc_start: 0.8518 (pp30) cc_final: 0.7864 (pp30) REVERT: E 6 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7755 (mm110) REVERT: K 367 CYS cc_start: 0.5885 (m) cc_final: 0.5561 (m) REVERT: N 6 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7981 (mm110) REVERT: H 50 ASP cc_start: 0.8237 (m-30) cc_final: 0.7952 (m-30) REVERT: H 65 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7593 (ttp-110) REVERT: H 73 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7915 (tt) REVERT: M 7 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.8021 (m) REVERT: M 50 ASP cc_start: 0.8421 (m-30) cc_final: 0.7863 (m-30) REVERT: M 55 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6818 (mm-30) outliers start: 108 outliers final: 78 residues processed: 417 average time/residue: 0.1437 time to fit residues: 95.2636 Evaluate side-chains 399 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 318 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 349 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 245 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 423 THR 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 22 CYS 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 74 THR Chi-restraints excluded: chain E residue 91 THR 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 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 55 VAL 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 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 398 SER 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 96 CYS 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 53 SER 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 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 M residue 73 LEU Chi-restraints excluded: chain P residue 29 THR 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 R residue 29 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 64 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 247 optimal weight: 0.3980 chunk 236 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 202 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 254 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN B 84 ASN C 183 ASN C 284 GLN G 74 ASN G 84 ASN K 284 GLN O 6 GLN M 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.147438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124748 restraints weight = 30683.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.125644 restraints weight = 25539.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126796 restraints weight = 21231.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127588 restraints weight = 17700.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127853 restraints weight = 15309.338| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21160 Z= 0.179 Angle : 0.629 10.687 28718 Z= 0.320 Chirality : 0.045 0.168 3330 Planarity : 0.004 0.058 3630 Dihedral : 4.707 41.824 2944 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 5.41 % Allowed : 19.48 % Favored : 75.11 % 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 aren not related in a simple way. whole: -1.80 (0.16), residues: 2652 helix: 0.24 (0.28), residues: 378 sheet: -0.63 (0.18), residues: 882 loop : -2.03 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 85 TYR 0.022 0.002 TYR R 86 PHE 0.018 0.002 PHE N 59 TRP 0.010 0.001 TRP B 113 HIS 0.009 0.002 HIS I 66 Details of bonding type rmsd covalent geometry : bond 0.00433 (21126) covalent geometry : angle 0.61609 (28647) SS BOND : bond 0.00427 ( 31) SS BOND : angle 1.73075 ( 62) hydrogen bonds : bond 0.03667 ( 669) hydrogen bonds : angle 5.39417 ( 1749) link_NAG-ASN : bond 0.00497 ( 3) link_NAG-ASN : angle 5.64895 ( 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 455 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 328 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7897 (p0) REVERT: D 90 GLN cc_start: 0.8638 (pp30) cc_final: 0.7977 (pp30) REVERT: E 6 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7566 (mm110) REVERT: F 79 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6214 (tt) REVERT: N 6 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7901 (mm110) REVERT: H 65 ARG cc_start: 0.8044 (ttm110) cc_final: 0.7627 (ttp-110) REVERT: H 73 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7876 (tt) REVERT: M 90 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7874 (pp30) outliers start: 127 outliers final: 98 residues processed: 421 average time/residue: 0.1373 time to fit residues: 93.0137 Evaluate side-chains 409 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 307 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 290 SER 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 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 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 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 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 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 300 VAL Chi-restraints excluded: chain K residue 349 VAL Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 398 SER Chi-restraints excluded: chain K residue 442 VAL 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 34 ILE Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS 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 96 ILE Chi-restraints excluded: chain O residue 106 ASP 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 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 90 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 113 optimal weight: 0.9990 chunk 182 optimal weight: 0.9990 chunk 213 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 167 optimal weight: 0.6980 chunk 212 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 116 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 284 GLN E 66 HIS I 6 GLN K 284 GLN O 6 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.151021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129015 restraints weight = 30356.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.129912 restraints weight = 20725.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.130687 restraints weight = 16180.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.130989 restraints weight = 14300.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131314 restraints weight = 13766.526| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21160 Z= 0.106 Angle : 0.587 9.669 28718 Z= 0.297 Chirality : 0.043 0.163 3330 Planarity : 0.004 0.055 3630 Dihedral : 4.451 38.882 2944 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.60 % Allowed : 20.67 % Favored : 74.72 % 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 aren not related in a simple way. whole: -1.57 (0.16), residues: 2652 helix: 0.82 (0.29), residues: 357 sheet: -0.76 (0.17), residues: 930 loop : -1.77 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 85 TYR 0.019 0.001 TYR B 53 PHE 0.013 0.001 PHE N 59 TRP 0.011 0.001 TRP K 314 HIS 0.017 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00241 (21126) covalent geometry : angle 0.57531 (28647) SS BOND : bond 0.00441 ( 31) SS BOND : angle 1.44784 ( 62) hydrogen bonds : bond 0.03023 ( 669) hydrogen bonds : angle 5.09731 ( 1749) link_NAG-ASN : bond 0.00489 ( 3) link_NAG-ASN : angle 5.56554 ( 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 435 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 327 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7893 (p0) REVERT: D 90 GLN cc_start: 0.8512 (pp30) cc_final: 0.7863 (pp30) REVERT: E 6 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7520 (mm110) REVERT: N 6 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7893 (mm110) REVERT: H 65 ARG cc_start: 0.8035 (ttm110) cc_final: 0.7629 (ttp-110) REVERT: H 73 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7880 (tt) REVERT: M 7 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8069 (m) REVERT: M 50 ASP cc_start: 0.8498 (m-30) cc_final: 0.7870 (m-30) outliers start: 108 outliers final: 89 residues processed: 402 average time/residue: 0.1369 time to fit residues: 87.9456 Evaluate side-chains 412 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 320 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 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 245 THR Chi-restraints excluded: chain C residue 335 THR 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 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 91 THR Chi-restraints excluded: chain E residue 110 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 68 SER 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 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 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 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 34 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS 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 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 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 72 THR 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 18 ARG Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain P residue 29 THR 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 R residue 29 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 64 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 233 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 220 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN C 183 ASN C 284 GLN K 284 GLN M 49 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.148006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.125945 restraints weight = 30611.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126857 restraints weight = 21210.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127200 restraints weight = 17377.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.127975 restraints weight = 16140.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128294 restraints weight = 13873.517| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 : 0.004 0.038 21160 Z= 0.160 Angle : 0.628 10.536 28718 Z= 0.319 Chirality : 0.044 0.167 3330 Planarity : 0.004 0.071 3630 Dihedral : 4.674 41.222 2944 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.86 % Allowed : 20.76 % Favored : 74.38 % 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 aren not related in a simple way. whole: -1.76 (0.16), residues: 2652 helix: 0.32 (0.28), residues: 378 sheet: -0.76 (0.18), residues: 918 loop : -1.91 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 85 TYR 0.021 0.001 TYR R 86 PHE 0.017 0.002 PHE E 59 TRP 0.011 0.001 TRP C 314 HIS 0.010 0.001 HIS I 66 Details of bonding type rmsd covalent geometry : bond 0.00384 (21126) covalent geometry : angle 0.61643 (28647) SS BOND : bond 0.00433 ( 31) SS BOND : angle 1.72787 ( 62) hydrogen bonds : bond 0.03461 ( 669) hydrogen bonds : angle 5.28583 ( 1749) link_NAG-ASN : bond 0.00435 ( 3) link_NAG-ASN : angle 5.46079 ( 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 431 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 317 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7454 (t80) REVERT: B 77 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.8049 (p0) REVERT: C 265 PRO cc_start: 0.8845 (Cg_exo) cc_final: 0.8575 (Cg_endo) REVERT: D 90 GLN cc_start: 0.8624 (pp30) cc_final: 0.8106 (pp30) REVERT: E 6 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7565 (mm110) REVERT: N 6 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7860 (mm110) REVERT: O 17 GLU cc_start: 0.7476 (tt0) cc_final: 0.7201 (tt0) REVERT: H 73 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7871 (tt) REVERT: M 50 ASP cc_start: 0.8834 (m-30) cc_final: 0.8194 (m-30) outliers start: 114 outliers final: 98 residues processed: 398 average time/residue: 0.1400 time to fit residues: 88.7671 Evaluate side-chains 412 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 311 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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 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 335 THR 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 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 110 ILE 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 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 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 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 34 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS 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 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 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 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 66 GLU Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.8041 > 50: distance: 10 - 158: 28.597 distance: 13 - 155: 29.837 distance: 64 - 137: 34.597 distance: 71 - 77: 34.224 distance: 77 - 78: 39.992 distance: 78 - 79: 51.185 distance: 79 - 80: 53.138 distance: 79 - 88: 18.923 distance: 81 - 82: 41.083 distance: 82 - 83: 14.126 distance: 82 - 84: 40.172 distance: 83 - 85: 15.580 distance: 84 - 86: 9.337 distance: 86 - 87: 32.522 distance: 88 - 89: 25.226 distance: 89 - 90: 50.592 distance: 89 - 92: 37.996 distance: 90 - 91: 34.244 distance: 90 - 96: 33.624 distance: 92 - 93: 39.520 distance: 93 - 94: 37.034 distance: 96 - 97: 40.928 distance: 96 - 102: 64.647 distance: 97 - 98: 16.676 distance: 97 - 100: 25.824 distance: 98 - 99: 59.020 distance: 98 - 103: 42.169 distance: 101 - 102: 41.536 distance: 103 - 104: 35.280 distance: 104 - 105: 5.868 distance: 104 - 107: 37.356 distance: 105 - 106: 48.532 distance: 105 - 112: 40.406 distance: 108 - 109: 52.631 distance: 109 - 110: 39.299 distance: 112 - 113: 39.444 distance: 113 - 114: 13.840 distance: 113 - 116: 17.502 distance: 114 - 115: 11.580 distance: 114 - 124: 48.703 distance: 116 - 117: 20.298 distance: 117 - 118: 34.702 distance: 117 - 119: 28.099 distance: 118 - 120: 34.700 distance: 120 - 122: 40.399 distance: 122 - 123: 3.830 distance: 125 - 126: 39.286 distance: 126 - 132: 23.544 distance: 128 - 129: 21.168 distance: 129 - 130: 34.656 distance: 129 - 131: 37.054 distance: 132 - 133: 17.639 distance: 133 - 134: 50.752 distance: 133 - 136: 40.429 distance: 134 - 135: 49.996 distance: 134 - 138: 38.733 distance: 136 - 137: 39.938 distance: 138 - 139: 7.984 distance: 139 - 142: 12.348 distance: 142 - 143: 28.627 distance: 143 - 144: 13.546 distance: 144 - 145: 15.516 distance: 147 - 148: 37.424 distance: 147 - 195: 36.001 distance: 148 - 149: 33.197 distance: 148 - 151: 50.060 distance: 149 - 150: 29.489 distance: 149 - 155: 25.832 distance: 150 - 192: 27.082 distance: 151 - 152: 26.908 distance: 151 - 153: 11.326 distance: 152 - 154: 42.701 distance: 155 - 156: 63.481 distance: 156 - 157: 38.963 distance: 156 - 159: 41.284 distance: 157 - 158: 41.576 distance: 157 - 163: 34.526 distance: 159 - 160: 38.241 distance: 160 - 161: 40.936 distance: 161 - 162: 54.981