Starting phenix.real_space_refine on Sat Mar 7 11:29:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hsr_35004/03_2026/8hsr_35004.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hsr_35004/03_2026/8hsr_35004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hsr_35004/03_2026/8hsr_35004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hsr_35004/03_2026/8hsr_35004.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hsr_35004/03_2026/8hsr_35004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hsr_35004/03_2026/8hsr_35004.map" } resolution = 4.0 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= -0.012 sd= 0.925 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 107 5.49 5 Mg 7 5.21 5 S 108 5.16 5 Be 6 3.05 5 C 26538 2.51 5 N 7594 2.21 5 O 8197 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42577 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "B" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "C" Number of atoms: 2882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2882 Classifications: {'peptide': 367} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 347} Chain: "D" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "E" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "F" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "G" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1806 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 214} Chain: "H" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1806 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 214} Chain: "I" Number of atoms: 8829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8829 Classifications: {'peptide': 1119} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1046} Chain: "J" Number of atoms: 10280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1303, 10280 Classifications: {'peptide': 1303} Link IDs: {'PTRANS': 62, 'TRANS': 1240} Chain breaks: 2 Chain: "K" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain: "T" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 786 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "R" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 474 Classifications: {'RNA': 29} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 20} Link IDs: {'rna3p': 28} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {' U%rna3p_pyr:plan': 3, ' A%rna3p_pur:plan': 6, ' A%rna3p_pur:plan2': 6, ' C%rna3p_pyr:plan': 5, ' C%rna3p_pyr:plan2': 5} Unresolved non-hydrogen planarities: 146 Chain: "N" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 574 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' MG': 2, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 30011 SG CYS J 58 88.040 122.955 93.958 1.00375.92 S ATOM 30022 SG CYS J 60 86.625 126.287 95.266 1.00419.37 S ATOM 30133 SG CYS J 73 86.654 125.732 91.839 1.00414.55 S ATOM 30159 SG CYS J 76 90.307 125.689 93.717 1.00409.45 S ATOM 36892 SG CYS J1112 134.528 88.458 62.611 1.00111.30 S ATOM 37536 SG CYS J1194 133.604 88.470 66.256 1.00 96.16 S ATOM 37592 SG CYS J1201 132.151 85.849 64.020 1.00101.97 S ATOM 37616 SG CYS J1204 135.611 85.441 64.747 1.00 97.92 S Time building chain proxies: 9.73, per 1000 atoms: 0.23 Number of scatterers: 42577 At special positions: 0 Unit cell: (201.4, 210.94, 168.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 108 16.00 P 107 15.00 Mg 7 11.99 F 18 9.00 O 8197 8.00 N 7594 7.00 C 26538 6.00 Be 6 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Atom "HETATM42407 O5' ADP A1000 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.12 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1601 " pdb="ZN ZN J1601 " - pdb=" SG CYS J 58 " pdb="ZN ZN J1601 " - pdb=" SG CYS J 60 " pdb="ZN ZN J1601 " - pdb=" SG CYS J 73 " pdb="ZN ZN J1601 " - pdb=" SG CYS J 76 " pdb=" ZN J1602 " pdb="ZN ZN J1602 " - pdb=" SG CYS J1201 " pdb="ZN ZN J1602 " - pdb=" SG CYS J1112 " pdb="ZN ZN J1602 " - pdb=" SG CYS J1204 " pdb="ZN ZN J1602 " - pdb=" SG CYS J1194 " Number of angles added : 12 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9526 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 62 sheets defined 43.1% alpha, 15.4% beta 21 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 5.68 Creating SS restraints... Processing helix chain 'A' and resid 91 through 99 Processing helix chain 'A' and resid 132 through 138 removed outlier: 3.657A pdb=" N ALA A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 189 through 205 Processing helix chain 'A' and resid 218 through 230 removed outlier: 3.944A pdb=" N GLN A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 263 Processing helix chain 'A' and resid 273 through 285 Processing helix chain 'A' and resid 297 through 310 removed outlier: 3.836A pdb=" N PHE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 332 through 344 removed outlier: 3.563A pdb=" N GLY A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 359 removed outlier: 3.559A pdb=" N GLU A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.605A pdb=" N LEU A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 395 Processing helix chain 'A' and resid 398 through 411 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'B' and resid 91 through 99 Processing helix chain 'B' and resid 132 through 138 removed outlier: 3.710A pdb=" N ASN B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.844A pdb=" N GLU B 144 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 172 removed outlier: 3.707A pdb=" N THR B 165 " --> pdb=" O ASP B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 205 Processing helix chain 'B' and resid 218 through 229 Processing helix chain 'B' and resid 242 through 263 Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 292 through 296 removed outlier: 4.179A pdb=" N LEU B 296 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 300 removed outlier: 3.996A pdb=" N ALA B 300 " --> pdb=" O ASP B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 332 through 344 Processing helix chain 'B' and resid 353 through 359 removed outlier: 3.885A pdb=" N GLU B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 359 " --> pdb=" O ARG B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.582A pdb=" N LEU B 378 " --> pdb=" O ARG B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 395 Processing helix chain 'B' and resid 398 through 413 removed outlier: 4.054A pdb=" N THR B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'C' and resid 91 through 99 Processing helix chain 'C' and resid 133 through 138 removed outlier: 3.535A pdb=" N LYS C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 145 Processing helix chain 'C' and resid 161 through 172 removed outlier: 3.778A pdb=" N THR C 165 " --> pdb=" O ASP C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 205 removed outlier: 3.510A pdb=" N LEU C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 229 Processing helix chain 'C' and resid 242 through 263 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 301 through 310 Processing helix chain 'C' and resid 332 through 344 Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 374 through 378 Processing helix chain 'C' and resid 380 through 397 Processing helix chain 'C' and resid 398 through 411 removed outlier: 3.744A pdb=" N ALA C 411 " --> pdb=" O LEU C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 426 Processing helix chain 'D' and resid 91 through 99 Processing helix chain 'D' and resid 132 through 138 removed outlier: 3.988A pdb=" N ALA D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.725A pdb=" N THR D 165 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 218 through 229 Processing helix chain 'D' and resid 242 through 263 Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 301 through 310 Processing helix chain 'D' and resid 332 through 344 Processing helix chain 'D' and resid 353 through 359 removed outlier: 3.542A pdb=" N GLU D 357 " --> pdb=" O SER D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.552A pdb=" N LEU D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 395 Processing helix chain 'D' and resid 398 through 413 removed outlier: 3.601A pdb=" N THR D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'E' and resid 91 through 99 Processing helix chain 'E' and resid 132 through 138 Processing helix chain 'E' and resid 141 through 145 Processing helix chain 'E' and resid 161 through 172 removed outlier: 3.544A pdb=" N THR E 165 " --> pdb=" O ASP E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 205 Processing helix chain 'E' and resid 218 through 229 Processing helix chain 'E' and resid 242 through 263 Processing helix chain 'E' and resid 273 through 285 Processing helix chain 'E' and resid 301 through 310 Processing helix chain 'E' and resid 332 through 344 Processing helix chain 'E' and resid 353 through 359 Processing helix chain 'E' and resid 374 through 378 Processing helix chain 'E' and resid 380 through 395 removed outlier: 3.660A pdb=" N ALA E 395 " --> pdb=" O ARG E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 413 removed outlier: 4.081A pdb=" N THR E 413 " --> pdb=" O ARG E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 420 Processing helix chain 'F' and resid 91 through 99 Processing helix chain 'F' and resid 127 through 131 removed outlier: 3.975A pdb=" N ASN F 130 " --> pdb=" O ALA F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 138 Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.652A pdb=" N THR F 165 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 205 Processing helix chain 'F' and resid 218 through 229 Processing helix chain 'F' and resid 242 through 263 Processing helix chain 'F' and resid 273 through 285 Processing helix chain 'F' and resid 301 through 310 Processing helix chain 'F' and resid 332 through 344 removed outlier: 3.619A pdb=" N ASP F 336 " --> pdb=" O SER F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 359 Processing helix chain 'F' and resid 374 through 379 Processing helix chain 'F' and resid 380 through 395 Processing helix chain 'F' and resid 398 through 412 removed outlier: 3.618A pdb=" N ARG F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 420 Processing helix chain 'G' and resid 32 through 47 Proline residue: G 39 - end of helix Processing helix chain 'G' and resid 74 through 84 removed outlier: 3.913A pdb=" N GLU G 84 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 114 removed outlier: 3.599A pdb=" N ASP G 113 " --> pdb=" O LYS G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 157 removed outlier: 3.657A pdb=" N HIS G 156 " --> pdb=" O PRO G 152 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY G 157 " --> pdb=" O ALA G 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 152 through 157' Processing helix chain 'G' and resid 206 through 223 Processing helix chain 'G' and resid 224 through 226 No H-bonds generated for 'chain 'G' and resid 224 through 226' Processing helix chain 'H' and resid 31 through 48 removed outlier: 3.643A pdb=" N THR H 35 " --> pdb=" O GLY H 31 " (cutoff:3.500A) Proline residue: H 39 - end of helix removed outlier: 4.309A pdb=" N ILE H 48 " --> pdb=" O LEU H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 84 removed outlier: 4.399A pdb=" N GLU H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 152 through 157 removed outlier: 4.419A pdb=" N HIS H 156 " --> pdb=" O PRO H 152 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY H 157 " --> pdb=" O ALA H 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 152 through 157' Processing helix chain 'H' and resid 206 through 223 Processing helix chain 'H' and resid 224 through 226 No H-bonds generated for 'chain 'H' and resid 224 through 226' Processing helix chain 'I' and resid 19 through 30 removed outlier: 3.644A pdb=" N VAL I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 79 through 86 Processing helix chain 'I' and resid 192 through 200 removed outlier: 4.334A pdb=" N LEU I 196 " --> pdb=" O PRO I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 211 Processing helix chain 'I' and resid 215 through 217 No H-bonds generated for 'chain 'I' and resid 215 through 217' Processing helix chain 'I' and resid 218 through 223 Processing helix chain 'I' and resid 232 through 242 removed outlier: 3.860A pdb=" N ILE I 236 " --> pdb=" O GLU I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 279 Processing helix chain 'I' and resid 302 through 316 Processing helix chain 'I' and resid 327 through 329 No H-bonds generated for 'chain 'I' and resid 327 through 329' Processing helix chain 'I' and resid 335 through 362 Processing helix chain 'I' and resid 375 through 389 removed outlier: 3.606A pdb=" N SER I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 431 through 435 removed outlier: 3.933A pdb=" N TYR I 435 " --> pdb=" O ARG I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 487 through 492 Processing helix chain 'I' and resid 525 through 529 Processing helix chain 'I' and resid 535 through 540 Processing helix chain 'I' and resid 541 through 546 removed outlier: 3.638A pdb=" N LEU I 546 " --> pdb=" O VAL I 542 " (cutoff:3.500A) Processing helix chain 'I' and resid 549 through 553 removed outlier: 3.601A pdb=" N HIS I 552 " --> pdb=" O PHE I 549 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 567 removed outlier: 3.717A pdb=" N THR I 566 " --> pdb=" O SER I 562 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN I 567 " --> pdb=" O ASN I 563 " (cutoff:3.500A) Processing helix chain 'I' and resid 583 through 591 Processing helix chain 'I' and resid 692 through 697 Processing helix chain 'I' and resid 732 through 737 removed outlier: 3.599A pdb=" N ARG I 735 " --> pdb=" O ALA I 732 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP I 736 " --> pdb=" O ALA I 733 " (cutoff:3.500A) Processing helix chain 'I' and resid 768 through 780 Processing helix chain 'I' and resid 854 through 858 removed outlier: 3.525A pdb=" N MET I 858 " --> pdb=" O VAL I 855 " (cutoff:3.500A) Processing helix chain 'I' and resid 874 through 879 removed outlier: 4.016A pdb=" N SER I 878 " --> pdb=" O LEU I 874 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG I 879 " --> pdb=" O GLY I 875 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 874 through 879' Processing helix chain 'I' and resid 882 through 898 removed outlier: 3.721A pdb=" N PHE I 896 " --> pdb=" O LEU I 892 " (cutoff:3.500A) Processing helix chain 'I' and resid 910 through 932 removed outlier: 3.762A pdb=" N GLU I 932 " --> pdb=" O LYS I 928 " (cutoff:3.500A) Processing helix chain 'I' and resid 937 through 950 Processing helix chain 'I' and resid 958 through 969 Processing helix chain 'I' and resid 1034 through 1043 Processing helix chain 'I' and resid 1046 through 1054 Processing helix chain 'I' and resid 1059 through 1072 Processing helix chain 'I' and resid 1082 through 1095 Processing helix chain 'J' and resid 14 through 22 Processing helix chain 'J' and resid 46 through 51 removed outlier: 3.528A pdb=" N PHE J 50 " --> pdb=" O ASP J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 89 Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.690A pdb=" N VAL J 105 " --> pdb=" O HIS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 116 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 155 through 163 removed outlier: 3.771A pdb=" N TYR J 163 " --> pdb=" O ARG J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 423 through 426 Processing helix chain 'J' and resid 456 through 468 removed outlier: 3.928A pdb=" N ALA J 460 " --> pdb=" O MET J 456 " (cutoff:3.500A) Processing helix chain 'J' and resid 469 through 483 removed outlier: 3.706A pdb=" N LEU J 473 " --> pdb=" O ASP J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 485 through 505 removed outlier: 3.503A pdb=" N ARG J 489 " --> pdb=" O SER J 485 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS J 491 " --> pdb=" O ALA J 487 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL J 498 " --> pdb=" O LYS J 494 " (cutoff:3.500A) Processing helix chain 'J' and resid 508 through 511 removed outlier: 3.735A pdb=" N TRP J 511 " --> pdb=" O ARG J 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 508 through 511' Processing helix chain 'J' and resid 521 through 525 Processing helix chain 'J' and resid 538 through 561 removed outlier: 3.835A pdb=" N ASP J 542 " --> pdb=" O SER J 538 " (cutoff:3.500A) Processing helix chain 'J' and resid 563 through 583 Processing helix chain 'J' and resid 602 through 608 Processing helix chain 'J' and resid 613 through 618 Processing helix chain 'J' and resid 646 through 653 Processing helix chain 'J' and resid 653 through 664 removed outlier: 3.629A pdb=" N LYS J 664 " --> pdb=" O LYS J 660 " (cutoff:3.500A) Processing helix chain 'J' and resid 669 through 678 Processing helix chain 'J' and resid 679 through 683 Processing helix chain 'J' and resid 684 through 695 Processing helix chain 'J' and resid 709 through 711 No H-bonds generated for 'chain 'J' and resid 709 through 711' Processing helix chain 'J' and resid 729 through 734 removed outlier: 4.280A pdb=" N GLU J 734 " --> pdb=" O LEU J 731 " (cutoff:3.500A) Processing helix chain 'J' and resid 752 through 763 Processing helix chain 'J' and resid 764 through 768 Processing helix chain 'J' and resid 782 through 793 Processing helix chain 'J' and resid 811 through 822 Processing helix chain 'J' and resid 835 through 841 Processing helix chain 'J' and resid 845 through 855 Processing helix chain 'J' and resid 876 through 890 Processing helix chain 'J' and resid 893 through 899 Processing helix chain 'J' and resid 907 through 922 Processing helix chain 'J' and resid 924 through 946 Processing helix chain 'J' and resid 950 through 954 Processing helix chain 'J' and resid 958 through 980 removed outlier: 3.907A pdb=" N GLN J 962 " --> pdb=" O GLU J 958 " (cutoff:3.500A) Processing helix chain 'J' and resid 984 through 1015 removed outlier: 3.701A pdb=" N GLU J1001 " --> pdb=" O THR J 997 " (cutoff:3.500A) Processing helix chain 'J' and resid 1018 through 1026 Processing helix chain 'J' and resid 1031 through 1040 Processing helix chain 'J' and resid 1066 through 1103 removed outlier: 3.838A pdb=" N HIS J1075 " --> pdb=" O PHE J1071 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY J1076 " --> pdb=" O ILE J1072 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA J1089 " --> pdb=" O ALA J1085 " (cutoff:3.500A) Processing helix chain 'J' and resid 1136 through 1145 Processing helix chain 'J' and resid 1167 through 1181 Processing helix chain 'J' and resid 1190 through 1194 Processing helix chain 'J' and resid 1201 through 1206 Processing helix chain 'J' and resid 1220 through 1231 removed outlier: 3.837A pdb=" N VAL J1224 " --> pdb=" O ALA J1220 " (cutoff:3.500A) Processing helix chain 'J' and resid 1232 through 1236 Processing helix chain 'J' and resid 1256 through 1264 Processing helix chain 'J' and resid 1331 through 1339 Processing helix chain 'J' and resid 1340 through 1359 removed outlier: 3.722A pdb=" N VAL J1355 " --> pdb=" O GLU J1351 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR J1356 " --> pdb=" O ILE J1352 " (cutoff:3.500A) Processing helix chain 'J' and resid 1364 through 1376 removed outlier: 4.531A pdb=" N ILE J1368 " --> pdb=" O HIS J1364 " (cutoff:3.500A) Processing helix chain 'J' and resid 1395 through 1407 Processing helix chain 'J' and resid 1423 through 1430 Processing helix chain 'J' and resid 1433 through 1441 removed outlier: 4.157A pdb=" N ALA J1437 " --> pdb=" O SER J1433 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN J1441 " --> pdb=" O ALA J1437 " (cutoff:3.500A) Processing helix chain 'J' and resid 1442 through 1453 removed outlier: 3.677A pdb=" N ALA J1453 " --> pdb=" O GLU J1449 " (cutoff:3.500A) Processing helix chain 'J' and resid 1461 through 1469 removed outlier: 3.876A pdb=" N ASN J1465 " --> pdb=" O GLY J1461 " (cutoff:3.500A) Processing helix chain 'J' and resid 1474 through 1477 Processing helix chain 'J' and resid 1478 through 1483 removed outlier: 4.618A pdb=" N PHE J1483 " --> pdb=" O ASP J1479 " (cutoff:3.500A) Processing helix chain 'J' and resid 1489 through 1503 removed outlier: 3.520A pdb=" N VAL J1503 " --> pdb=" O ARG J1499 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 12 Processing helix chain 'K' and resid 15 through 34 removed outlier: 3.541A pdb=" N LEU K 19 " --> pdb=" O SER K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 56 Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 81 through 89 removed outlier: 3.958A pdb=" N LEU K 85 " --> pdb=" O PRO K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 110 removed outlier: 6.690A pdb=" N GLN A 109 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 125 " --> pdb=" O GLN A 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 154 removed outlier: 4.355A pdb=" N ILE A 174 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 233 through 237 removed outlier: 6.879A pdb=" N VAL A 210 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE A 235 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 212 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N SER A 237 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 214 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 209 " --> pdb=" O HIS A 266 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR A 325 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A 180 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA A 324 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET A 348 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N GLU A 349 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU A 368 " --> pdb=" O GLU A 349 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS A 351 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 74 through 77 removed outlier: 6.488A pdb=" N TYR B 105 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA B 127 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL B 107 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL B 125 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN B 109 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 148 removed outlier: 3.769A pdb=" N ASN B 313 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 233 through 237 removed outlier: 6.749A pdb=" N VAL B 210 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE B 235 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL B 212 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N SER B 237 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B 214 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS B 209 " --> pdb=" O MET B 268 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU B 270 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 211 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 325 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE B 182 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N GLU B 349 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N LEU B 368 " --> pdb=" O GLU B 349 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N HIS B 351 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 61 through 65 removed outlier: 6.103A pdb=" N GLN C 109 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N VAL C 125 " --> pdb=" O GLN C 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.758A pdb=" N ASN C 313 " --> pdb=" O GLN C 148 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 233 through 238 removed outlier: 6.879A pdb=" N VAL C 210 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE C 235 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL C 212 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER C 237 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU C 214 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLY C 180 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ALA C 326 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE C 182 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N GLU C 349 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N LEU C 368 " --> pdb=" O GLU C 349 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS C 351 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 75 through 77 removed outlier: 3.762A pdb=" N TYR D 65 " --> pdb=" O THR D 77 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 147 through 148 removed outlier: 3.633A pdb=" N ASN D 313 " --> pdb=" O GLN D 148 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU D 233 " --> pdb=" O VAL D 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 147 through 148 removed outlier: 3.633A pdb=" N ASN D 313 " --> pdb=" O GLN D 148 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N GLU D 349 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N LEU D 368 " --> pdb=" O GLU D 349 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N HIS D 351 " --> pdb=" O ASP D 366 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 62 through 64 Processing sheet with id=AB8, first strand: chain 'E' and resid 147 through 148 removed outlier: 3.616A pdb=" N ASN E 313 " --> pdb=" O GLN E 148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 153 through 154 removed outlier: 4.514A pdb=" N ILE E 174 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 233 through 235 removed outlier: 7.211A pdb=" N VAL E 210 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ILE E 235 " --> pdb=" O VAL E 210 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL E 212 " --> pdb=" O ILE E 235 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE E 182 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU E 349 " --> pdb=" O GLY E 371 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY E 371 " --> pdb=" O GLU E 349 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 62 through 65 removed outlier: 3.687A pdb=" N VAL F 62 " --> pdb=" O GLY F 108 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY F 108 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS F 124 " --> pdb=" O GLN F 109 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 147 through 148 removed outlier: 3.672A pdb=" N ASN F 313 " --> pdb=" O GLN F 148 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 179 through 184 removed outlier: 3.807A pdb=" N GLY F 180 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA F 324 " --> pdb=" O GLY F 180 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 348 through 352 removed outlier: 9.016A pdb=" N GLU F 349 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N LEU F 368 " --> pdb=" O GLU F 349 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS F 351 " --> pdb=" O ASP F 366 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 10 through 16 removed outlier: 3.672A pdb=" N TYR G 20 " --> pdb=" O GLN G 16 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N TYR G 20 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR G 201 " --> pdb=" O TYR G 20 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU G 22 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE G 199 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL G 24 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU G 197 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU G 26 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU G 195 " --> pdb=" O GLU G 26 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 96 through 104 removed outlier: 7.677A pdb=" N ASN G 139 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE G 58 " --> pdb=" O ASN G 139 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU G 141 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL G 56 " --> pdb=" O GLU G 141 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG G 143 " --> pdb=" O THR G 54 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 87 through 89 Processing sheet with id=AC9, first strand: chain 'G' and resid 150 through 151 Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 16 removed outlier: 3.511A pdb=" N TYR H 20 " --> pdb=" O GLN H 16 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR H 20 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR H 201 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLU H 22 " --> pdb=" O ILE H 199 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE H 199 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL H 24 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU H 197 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLU H 26 " --> pdb=" O LEU H 195 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU H 195 " --> pdb=" O GLU H 26 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 96 through 103 removed outlier: 7.629A pdb=" N ASN H 139 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ILE H 58 " --> pdb=" O ASN H 139 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU H 141 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL H 56 " --> pdb=" O GLU H 141 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG H 143 " --> pdb=" O THR H 54 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AD4, first strand: chain 'H' and resid 108 through 110 Processing sheet with id=AD5, first strand: chain 'H' and resid 150 through 151 Processing sheet with id=AD6, first strand: chain 'I' and resid 3 through 5 removed outlier: 6.265A pdb=" N LYS I 4 " --> pdb=" O ILE I 902 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 54 through 56 removed outlier: 5.302A pdb=" N LEU I 66 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE I 101 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N PHE I 68 " --> pdb=" O GLN I 99 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN I 99 " --> pdb=" O PHE I 68 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ALA I 92 " --> pdb=" O GLY I 116 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLY I 116 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU I 94 " --> pdb=" O PHE I 114 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE I 114 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA I 96 " --> pdb=" O GLU I 112 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU I 112 " --> pdb=" O ALA I 96 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AD9, first strand: chain 'I' and resid 331 through 334 removed outlier: 6.318A pdb=" N SER I 138 " --> pdb=" O SER I 411 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 145 through 150 removed outlier: 6.367A pdb=" N TYR I 158 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL I 176 " --> pdb=" O TYR I 158 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 460 through 461 removed outlier: 5.931A pdb=" N GLU I 482 " --> pdb=" O ARG I 473 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL I 475 " --> pdb=" O THR I 480 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR I 480 " --> pdb=" O VAL I 475 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 460 through 461 Processing sheet with id=AE4, first strand: chain 'I' and resid 513 through 516 Processing sheet with id=AE5, first strand: chain 'I' and resid 595 through 596 removed outlier: 6.538A pdb=" N LEU I 595 " --> pdb=" O LEU I 655 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 620 through 624 removed outlier: 5.832A pdb=" N ARG I 614 " --> pdb=" O VAL I 603 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL I 603 " --> pdb=" O ARG I 614 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 629 through 630 Processing sheet with id=AE8, first strand: chain 'I' and resid 971 through 972 removed outlier: 7.165A pdb=" N ILE I 688 " --> pdb=" O ALA I 850 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE I 852 " --> pdb=" O ILE I 688 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE I 690 " --> pdb=" O ILE I 852 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N VAL I 869 " --> pdb=" O ASN I 671 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU I 673 " --> pdb=" O VAL I 869 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU I 871 " --> pdb=" O LEU I 673 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA I 675 " --> pdb=" O LEU I 871 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL I 988 " --> pdb=" O ILE I 676 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 718 through 719 removed outlier: 5.934A pdb=" N ASP I 714 " --> pdb=" O VAL I 819 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL I 819 " --> pdb=" O ASP I 714 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL I 822 " --> pdb=" O ARG I 805 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG I 805 " --> pdb=" O VAL I 822 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG I 824 " --> pdb=" O THR I 803 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR I 803 " --> pdb=" O ARG I 824 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR I 826 " --> pdb=" O VAL I 801 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 721 through 722 Processing sheet with id=AF2, first strand: chain 'I' and resid 754 through 756 removed outlier: 7.044A pdb=" N LEU I 790 " --> pdb=" O LEU I 755 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 1099 through 1102 Processing sheet with id=AF4, first strand: chain 'J' and resid 91 through 100 removed outlier: 6.965A pdb=" N GLU J 515 " --> pdb=" O LEU J 95 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N THR J 97 " --> pdb=" O ILE J 513 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N ILE J 513 " --> pdb=" O THR J 97 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 132 through 133 removed outlier: 3.541A pdb=" N ILE J 133 " --> pdb=" O LEU J 153 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU J 153 " --> pdb=" O ILE J 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'J' and resid 166 through 170 removed outlier: 3.748A pdb=" N GLU J 183 " --> pdb=" O ALA J 203 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 399 through 402 Processing sheet with id=AF8, first strand: chain 'J' and resid 420 through 422 removed outlier: 7.487A pdb=" N VAL J 427 " --> pdb=" O LEU J 421 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 528 through 529 Processing sheet with id=AG1, first strand: chain 'J' and resid 626 through 633 Processing sheet with id=AG2, first strand: chain 'J' and resid 842 through 843 removed outlier: 7.269A pdb=" N PHE J 843 " --> pdb=" O ARG J 867 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 1118 through 1121 Processing sheet with id=AG4, first strand: chain 'J' and resid 1123 through 1124 removed outlier: 3.712A pdb=" N ARG J1133 " --> pdb=" O GLN J1124 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 1153 through 1154 Processing sheet with id=AG6, first strand: chain 'J' and resid 1300 through 1305 Processing sheet with id=AG7, first strand: chain 'J' and resid 1392 through 1394 removed outlier: 4.390A pdb=" N TYR J1378 " --> pdb=" O LEU J1420 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 1486 through 1488 removed outlier: 3.849A pdb=" N VAL J1487 " --> pdb=" O VAL K 74 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL K 74 " --> pdb=" O VAL J1487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 1756 hydrogen bonds defined for protein. 4950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 12.63 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9225 1.33 - 1.45: 9069 1.45 - 1.57: 24763 1.57 - 1.69: 204 1.69 - 1.82: 203 Bond restraints: 43464 Sorted by residual: bond pdb=" F2 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" F2 BEF D1002 " pdb="BE BEF D1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" F2 BEF E1002 " pdb="BE BEF E1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F2 BEF F1002 " pdb="BE BEF F1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F2 BEF C1004 " pdb="BE BEF C1004 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 43459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 58311 2.76 - 5.52: 760 5.52 - 8.29: 78 8.29 - 11.05: 15 11.05 - 13.81: 9 Bond angle restraints: 59173 Sorted by residual: angle pdb=" N GLN F 97 " pdb=" CA GLN F 97 " pdb=" CB GLN F 97 " ideal model delta sigma weight residual 110.07 117.42 -7.35 1.45e+00 4.76e-01 2.57e+01 angle pdb=" N GLU E 78 " pdb=" CA GLU E 78 " pdb=" C GLU E 78 " ideal model delta sigma weight residual 108.07 114.79 -6.72 1.38e+00 5.25e-01 2.37e+01 angle pdb=" N VAL I 254 " pdb=" CA VAL I 254 " pdb=" C VAL I 254 " ideal model delta sigma weight residual 113.42 107.87 5.55 1.17e+00 7.31e-01 2.25e+01 angle pdb=" C3' DC T 21 " pdb=" O3' DC T 21 " pdb=" P DA T 22 " ideal model delta sigma weight residual 120.20 127.21 -7.01 1.50e+00 4.44e-01 2.18e+01 angle pdb=" F2 BEF B 502 " pdb="BE BEF B 502 " pdb=" F3 BEF B 502 " ideal model delta sigma weight residual 119.96 106.27 13.69 3.00e+00 1.11e-01 2.08e+01 ... (remaining 59168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 26030 35.65 - 71.30: 588 71.30 - 106.96: 43 106.96 - 142.61: 2 142.61 - 178.26: 5 Dihedral angle restraints: 26668 sinusoidal: 11892 harmonic: 14776 Sorted by residual: dihedral pdb=" C4' U R 13 " pdb=" C3' U R 13 " pdb=" C2' U R 13 " pdb=" C1' U R 13 " ideal model delta sinusoidal sigma weight residual 36.00 -36.29 72.29 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" C5' U R 13 " pdb=" C4' U R 13 " pdb=" C3' U R 13 " pdb=" O3' U R 13 " ideal model delta sinusoidal sigma weight residual 82.00 148.37 -66.37 1 8.00e+00 1.56e-02 8.99e+01 dihedral pdb=" O4' U R 13 " pdb=" C2' U R 13 " pdb=" C1' U R 13 " pdb=" C3' U R 13 " ideal model delta sinusoidal sigma weight residual 25.00 -36.01 61.01 1 8.00e+00 1.56e-02 7.73e+01 ... (remaining 26665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 5599 0.061 - 0.123: 1066 0.123 - 0.184: 86 0.184 - 0.246: 5 0.246 - 0.307: 4 Chirality restraints: 6760 Sorted by residual: chirality pdb=" CG LEU J 619 " pdb=" CB LEU J 619 " pdb=" CD1 LEU J 619 " pdb=" CD2 LEU J 619 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB ILE I 163 " pdb=" CA ILE I 163 " pdb=" CG1 ILE I 163 " pdb=" CG2 ILE I 163 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" P DG T 32 " pdb=" OP1 DG T 32 " pdb=" OP2 DG T 32 " pdb=" O5' DG T 32 " both_signs ideal model delta sigma weight residual True 2.35 -2.62 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 6757 not shown) Planarity restraints: 7415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 286 " 0.083 5.00e-02 4.00e+02 1.28e-01 2.60e+01 pdb=" N PRO B 287 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO B 287 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO B 287 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 286 " 0.056 5.00e-02 4.00e+02 8.46e-02 1.14e+01 pdb=" N PRO C 287 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO C 287 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 287 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP K 57 " -0.045 5.00e-02 4.00e+02 6.74e-02 7.26e+00 pdb=" N PRO K 58 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO K 58 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO K 58 " -0.038 5.00e-02 4.00e+02 ... (remaining 7412 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 35 1.97 - 2.71: 2079 2.71 - 3.44: 66359 3.44 - 4.17: 106025 4.17 - 4.90: 182290 Nonbonded interactions: 356788 Sorted by model distance: nonbonded pdb=" OE2 GLU B 217 " pdb=" F1 BEF B 502 " model vdw 1.243 2.990 nonbonded pdb=" OE2 GLU B 217 " pdb="BE BEF B 502 " model vdw 1.301 2.420 nonbonded pdb=" O2B ADP A1000 " pdb=" F2 BEF A1002 " model vdw 1.328 2.990 nonbonded pdb=" C2 DG T 1 " pdb=" O2 DC N 41 " model vdw 1.354 3.260 nonbonded pdb=" N1 DG T 1 " pdb=" O2 DC N 41 " model vdw 1.380 3.120 ... (remaining 356783 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 60 through 1000) selection = (chain 'B' and resid 60 through 501) selection = (chain 'C' and (resid 60 through 420 or resid 1002)) selection = (chain 'D' and resid 60 through 1000) selection = (chain 'E' and resid 60 through 1000) selection = (chain 'F' and resid 60 through 1000) } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 52.400 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5645 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 : 0.006 0.644 43482 Z= 0.415 Angle : 0.809 13.809 59185 Z= 0.414 Chirality : 0.046 0.307 6760 Planarity : 0.006 0.128 7415 Dihedral : 15.148 178.259 17142 Min Nonbonded Distance : 1.243 Molprobity Statistics. All-atom Clashscore : 24.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.70 % Favored : 93.14 % Rotamer: Outliers : 0.02 % Allowed : 0.41 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.12), residues: 5117 helix: 0.24 (0.12), residues: 1835 sheet: -0.59 (0.19), residues: 710 loop : -0.92 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 276 TYR 0.033 0.002 TYR B 98 PHE 0.037 0.002 PHE B 252 TRP 0.030 0.003 TRP D 388 HIS 0.010 0.002 HIS J1103 Details of bonding type rmsd covalent geometry : bond 0.00493 (43464) covalent geometry : angle 0.80201 (59173) hydrogen bonds : bond 0.18457 ( 1802) hydrogen bonds : angle 7.48166 ( 5048) metal coordination : bond 0.01411 ( 8) metal coordination : angle 7.60002 ( 12) Misc. bond : bond 0.22732 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 318 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 140 MET cc_start: 0.7886 (ppp) cc_final: 0.7457 (ppp) REVERT: J 456 MET cc_start: 0.4600 (ttt) cc_final: 0.4228 (ttp) REVERT: J 661 MET cc_start: 0.9106 (ppp) cc_final: 0.8704 (ppp) REVERT: J 1219 GLU cc_start: 0.8445 (pp20) cc_final: 0.8188 (pp20) outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.2562 time to fit residues: 139.5736 Evaluate side-chains 222 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 0.0070 chunk 265 optimal weight: 9.9990 chunk 497 optimal weight: 0.9990 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 10.0000 chunk 366 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 chunk 516 optimal weight: 10.0000 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 313 ASN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN C 97 GLN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 HIS ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 HIS ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN J 593 ASN J1010 ASN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.061827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.045653 restraints weight = 302488.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.046953 restraints weight = 177755.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.047816 restraints weight = 125779.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.048393 restraints weight = 99236.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.048774 restraints weight = 84734.991| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 43482 Z= 0.178 Angle : 0.739 12.875 59185 Z= 0.371 Chirality : 0.046 0.215 6760 Planarity : 0.006 0.124 7415 Dihedral : 14.438 172.314 6870 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.29 % Favored : 93.63 % Rotamer: Outliers : 0.74 % Allowed : 7.90 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.12), residues: 5117 helix: 0.19 (0.12), residues: 1947 sheet: -0.62 (0.19), residues: 719 loop : -0.95 (0.13), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 276 TYR 0.029 0.002 TYR J1207 PHE 0.026 0.002 PHE F 362 TRP 0.019 0.002 TRP J 21 HIS 0.006 0.001 HIS E 81 Details of bonding type rmsd covalent geometry : bond 0.00387 (43464) covalent geometry : angle 0.73356 (59173) hydrogen bonds : bond 0.05317 ( 1802) hydrogen bonds : angle 6.09655 ( 5048) metal coordination : bond 0.00929 ( 8) metal coordination : angle 6.49887 ( 12) Misc. bond : bond 0.00240 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.9345 (mp0) cc_final: 0.8836 (mp0) REVERT: A 397 MET cc_start: 0.6659 (tmm) cc_final: 0.6360 (tmm) REVERT: A 405 MET cc_start: 0.8750 (ppp) cc_final: 0.8375 (ppp) REVERT: B 268 MET cc_start: 0.8747 (tpp) cc_final: 0.8503 (tpp) REVERT: B 397 MET cc_start: 0.6691 (pmm) cc_final: 0.6245 (pmm) REVERT: C 105 TYR cc_start: 0.7737 (t80) cc_final: 0.7517 (t80) REVERT: D 387 MET cc_start: 0.7821 (ptt) cc_final: 0.6879 (ppp) REVERT: E 225 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8841 (t80) REVERT: E 405 MET cc_start: 0.9447 (tmm) cc_final: 0.8948 (ppp) REVERT: G 1 MET cc_start: 0.6925 (ptp) cc_final: 0.6707 (mmt) REVERT: G 163 ASN cc_start: 0.8776 (t0) cc_final: 0.8363 (t0) REVERT: I 560 MET cc_start: 0.8525 (ptm) cc_final: 0.8140 (ptp) REVERT: I 880 MET cc_start: 0.8094 (mpp) cc_final: 0.7875 (mpp) REVERT: I 1031 ARG cc_start: 0.7794 (mpt180) cc_final: 0.7495 (mmt180) REVERT: I 1035 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8400 (mtt) REVERT: J 456 MET cc_start: 0.4810 (ttt) cc_final: 0.4578 (ttp) REVERT: J 661 MET cc_start: 0.9294 (ppp) cc_final: 0.8827 (ppp) REVERT: J 1219 GLU cc_start: 0.8838 (pp20) cc_final: 0.8416 (pp20) REVERT: K 52 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7564 (mm-30) outliers start: 32 outliers final: 15 residues processed: 272 average time/residue: 0.2484 time to fit residues: 116.7696 Evaluate side-chains 236 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 219 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 1035 MET Chi-restraints excluded: chain I residue 1106 ASP Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 713 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 369 optimal weight: 9.9990 chunk 491 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 93 optimal weight: 0.0570 chunk 240 optimal weight: 10.0000 chunk 417 optimal weight: 7.9990 chunk 375 optimal weight: 0.9990 chunk 305 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 350 optimal weight: 6.9990 chunk 401 optimal weight: 6.9990 overall best weight: 3.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN E 347 ASN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 ASN I 31 GLN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.061241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.045057 restraints weight = 301441.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.046354 restraints weight = 179046.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.047160 restraints weight = 126847.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.047717 restraints weight = 101225.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.048078 restraints weight = 87216.397| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 43482 Z= 0.168 Angle : 0.684 11.641 59185 Z= 0.341 Chirality : 0.044 0.200 6760 Planarity : 0.005 0.122 7415 Dihedral : 14.261 176.683 6870 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.45 % Favored : 93.47 % Rotamer: Outliers : 1.03 % Allowed : 10.87 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.12), residues: 5117 helix: 0.29 (0.12), residues: 1951 sheet: -0.70 (0.19), residues: 735 loop : -0.90 (0.13), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 276 TYR 0.027 0.001 TYR J1207 PHE 0.023 0.002 PHE F 362 TRP 0.019 0.001 TRP J 21 HIS 0.014 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00370 (43464) covalent geometry : angle 0.67864 (59173) hydrogen bonds : bond 0.04718 ( 1802) hydrogen bonds : angle 5.80511 ( 5048) metal coordination : bond 0.00938 ( 8) metal coordination : angle 5.92896 ( 12) Misc. bond : bond 0.00156 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 238 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.9160 (mp0) cc_final: 0.8783 (mp0) REVERT: A 348 MET cc_start: 0.7638 (mmm) cc_final: 0.7260 (mmm) REVERT: A 405 MET cc_start: 0.8757 (ppp) cc_final: 0.8303 (ppp) REVERT: B 268 MET cc_start: 0.8753 (tpp) cc_final: 0.8502 (tpp) REVERT: B 270 LEU cc_start: 0.8914 (mp) cc_final: 0.8190 (mt) REVERT: B 348 MET cc_start: 0.7431 (mmm) cc_final: 0.6353 (mmm) REVERT: B 397 MET cc_start: 0.6877 (pmm) cc_final: 0.6666 (pmm) REVERT: C 105 TYR cc_start: 0.7910 (t80) cc_final: 0.7687 (t80) REVERT: C 225 PHE cc_start: 0.9305 (t80) cc_final: 0.8690 (t80) REVERT: D 132 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8760 (t0) REVERT: D 387 MET cc_start: 0.7725 (ptt) cc_final: 0.6818 (ppp) REVERT: E 225 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8888 (t80) REVERT: F 403 MET cc_start: 0.9182 (tmm) cc_final: 0.8651 (tmm) REVERT: G 1 MET cc_start: 0.6992 (ptp) cc_final: 0.6773 (mmt) REVERT: G 163 ASN cc_start: 0.8847 (t0) cc_final: 0.8550 (t0) REVERT: I 340 MET cc_start: 0.8780 (tmm) cc_final: 0.8302 (tmm) REVERT: I 564 MET cc_start: 0.8598 (mtt) cc_final: 0.8281 (mpp) REVERT: I 880 MET cc_start: 0.8070 (mpp) cc_final: 0.7860 (mpp) REVERT: J 481 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8771 (tpp) REVERT: J 573 MET cc_start: 0.9278 (mtm) cc_final: 0.9054 (mtm) REVERT: J 661 MET cc_start: 0.9223 (ppp) cc_final: 0.8817 (ppp) REVERT: J 980 MET cc_start: 0.8383 (mmt) cc_final: 0.8170 (mmt) REVERT: J 1219 GLU cc_start: 0.8846 (pp20) cc_final: 0.8410 (pp20) REVERT: K 29 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8565 (mp10) REVERT: K 88 GLU cc_start: 0.7313 (tp30) cc_final: 0.6139 (pt0) outliers start: 45 outliers final: 24 residues processed: 270 average time/residue: 0.2523 time to fit residues: 116.9617 Evaluate side-chains 242 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 1097 LEU Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 481 MET Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 713 ILE Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 47 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 423 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 447 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 465 optimal weight: 5.9990 chunk 293 optimal weight: 9.9990 chunk 146 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 421 optimal weight: 8.9990 chunk 441 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN B 347 ASN C 97 GLN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 ASN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 ASN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 909 ASN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.059190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.043112 restraints weight = 305285.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.044302 restraints weight = 183390.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.045128 restraints weight = 131642.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.045640 restraints weight = 105371.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.045925 restraints weight = 91223.695| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 43482 Z= 0.248 Angle : 0.727 10.987 59185 Z= 0.364 Chirality : 0.044 0.189 6760 Planarity : 0.006 0.122 7415 Dihedral : 14.212 179.711 6870 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.96 % Favored : 92.96 % Rotamer: Outliers : 1.82 % Allowed : 12.98 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.12), residues: 5117 helix: 0.26 (0.12), residues: 1957 sheet: -0.73 (0.19), residues: 722 loop : -0.97 (0.13), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 276 TYR 0.029 0.002 TYR J1207 PHE 0.022 0.002 PHE C 252 TRP 0.027 0.002 TRP J 21 HIS 0.006 0.001 HIS J1075 Details of bonding type rmsd covalent geometry : bond 0.00540 (43464) covalent geometry : angle 0.72250 (59173) hydrogen bonds : bond 0.04897 ( 1802) hydrogen bonds : angle 5.80545 ( 5048) metal coordination : bond 0.01373 ( 8) metal coordination : angle 5.86089 ( 12) Misc. bond : bond 0.00152 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 220 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 MET cc_start: 0.8094 (mmm) cc_final: 0.7776 (mmm) REVERT: A 405 MET cc_start: 0.8809 (ppp) cc_final: 0.8444 (ppp) REVERT: B 338 ILE cc_start: 0.9295 (mt) cc_final: 0.9047 (pt) REVERT: B 348 MET cc_start: 0.7973 (mmm) cc_final: 0.6982 (mmm) REVERT: B 397 MET cc_start: 0.7241 (pmm) cc_final: 0.6881 (pmm) REVERT: B 405 MET cc_start: 0.8818 (ppp) cc_final: 0.8473 (ppp) REVERT: C 397 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7157 (tmm) REVERT: D 132 ASP cc_start: 0.9018 (OUTLIER) cc_final: 0.8722 (t0) REVERT: D 183 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8562 (m) REVERT: D 277 LEU cc_start: 0.9566 (tp) cc_final: 0.9229 (mt) REVERT: D 387 MET cc_start: 0.7856 (ptt) cc_final: 0.6965 (ppp) REVERT: E 66 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.6661 (tt) REVERT: E 97 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8562 (pt0) REVERT: E 225 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8905 (t80) REVERT: E 348 MET cc_start: 0.7884 (mmm) cc_final: 0.6887 (mpp) REVERT: E 397 MET cc_start: 0.8389 (tmm) cc_final: 0.8037 (tmm) REVERT: E 405 MET cc_start: 0.9536 (tmm) cc_final: 0.8940 (ppp) REVERT: G 1 MET cc_start: 0.7110 (ptp) cc_final: 0.6837 (mmt) REVERT: G 163 ASN cc_start: 0.8969 (t0) cc_final: 0.8746 (t0) REVERT: H 140 MET cc_start: 0.8307 (ppp) cc_final: 0.7016 (ppp) REVERT: I 99 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8589 (pp30) REVERT: I 340 MET cc_start: 0.8859 (tmm) cc_final: 0.8397 (tmm) REVERT: I 564 MET cc_start: 0.8599 (mtt) cc_final: 0.8331 (mpp) REVERT: I 1047 HIS cc_start: 0.7030 (OUTLIER) cc_final: 0.6677 (m90) REVERT: J 481 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8801 (tpp) REVERT: J 661 MET cc_start: 0.9119 (ppp) cc_final: 0.8691 (ppp) REVERT: J 1219 GLU cc_start: 0.8895 (pp20) cc_final: 0.8433 (pp20) REVERT: K 52 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7560 (mm-30) REVERT: K 88 GLU cc_start: 0.7553 (tp30) cc_final: 0.6286 (pt0) outliers start: 79 outliers final: 43 residues processed: 280 average time/residue: 0.2333 time to fit residues: 113.5513 Evaluate side-chains 260 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain C residue 426 ARG Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 385 HIS Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 313 ASN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 1006 HIS Chi-restraints excluded: chain I residue 1047 HIS Chi-restraints excluded: chain I residue 1097 LEU Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 481 MET Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 713 ILE Chi-restraints excluded: chain K residue 29 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 134 optimal weight: 8.9990 chunk 410 optimal weight: 10.0000 chunk 295 optimal weight: 8.9990 chunk 504 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 485 optimal weight: 7.9990 chunk 461 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 351 optimal weight: 2.9990 chunk 153 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1334 GLN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.059329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.043255 restraints weight = 303615.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.044494 restraints weight = 179241.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.045267 restraints weight = 127168.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.045825 restraints weight = 101866.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.046162 restraints weight = 87424.524| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 43482 Z= 0.192 Angle : 0.688 10.609 59185 Z= 0.341 Chirality : 0.044 0.228 6760 Planarity : 0.005 0.120 7415 Dihedral : 14.077 178.030 6870 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.27 % Favored : 93.65 % Rotamer: Outliers : 2.21 % Allowed : 14.11 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.12), residues: 5117 helix: 0.36 (0.12), residues: 1952 sheet: -0.75 (0.19), residues: 692 loop : -0.95 (0.13), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 276 TYR 0.029 0.002 TYR J1207 PHE 0.023 0.002 PHE C 252 TRP 0.035 0.002 TRP J 21 HIS 0.005 0.001 HIS J1364 Details of bonding type rmsd covalent geometry : bond 0.00422 (43464) covalent geometry : angle 0.68342 (59173) hydrogen bonds : bond 0.04386 ( 1802) hydrogen bonds : angle 5.62540 ( 5048) metal coordination : bond 0.01066 ( 8) metal coordination : angle 5.32198 ( 12) Misc. bond : bond 0.00148 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 230 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8394 (t80) cc_final: 0.8151 (t80) REVERT: A 405 MET cc_start: 0.8941 (ppp) cc_final: 0.8638 (ppp) REVERT: B 61 LEU cc_start: 0.9071 (tt) cc_final: 0.8706 (mm) REVERT: B 268 MET cc_start: 0.8875 (tpp) cc_final: 0.8398 (tpp) REVERT: B 348 MET cc_start: 0.8158 (mmm) cc_final: 0.7089 (mmm) REVERT: B 403 MET cc_start: 0.8893 (mmm) cc_final: 0.8681 (mmm) REVERT: B 405 MET cc_start: 0.8815 (ppp) cc_final: 0.8473 (ppp) REVERT: C 397 MET cc_start: 0.7797 (ptm) cc_final: 0.7303 (tmm) REVERT: D 105 TYR cc_start: 0.9173 (t80) cc_final: 0.8705 (t80) REVERT: D 132 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8833 (t0) REVERT: D 183 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8577 (m) REVERT: D 387 MET cc_start: 0.7926 (ptt) cc_final: 0.7111 (ppp) REVERT: E 66 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.6972 (tt) REVERT: E 100 LEU cc_start: 0.7800 (mt) cc_final: 0.7597 (mt) REVERT: E 225 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8953 (t80) REVERT: E 348 MET cc_start: 0.7882 (mmm) cc_final: 0.7267 (mpp) REVERT: E 397 MET cc_start: 0.8367 (tmm) cc_final: 0.8010 (tmm) REVERT: F 348 MET cc_start: 0.7696 (mmm) cc_final: 0.7197 (mmm) REVERT: G 1 MET cc_start: 0.7052 (ptp) cc_final: 0.6783 (mmt) REVERT: G 163 ASN cc_start: 0.8982 (t0) cc_final: 0.8726 (t0) REVERT: H 140 MET cc_start: 0.8385 (ppp) cc_final: 0.7344 (ppp) REVERT: I 99 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8704 (pp30) REVERT: I 184 MET cc_start: 0.8416 (ppp) cc_final: 0.8210 (tmm) REVERT: I 340 MET cc_start: 0.8895 (tmm) cc_final: 0.8413 (tmm) REVERT: I 880 MET cc_start: 0.8054 (mpp) cc_final: 0.7793 (mpp) REVERT: J 90 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8164 (tpp) REVERT: J 481 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8828 (tpp) REVERT: J 661 MET cc_start: 0.9160 (ppp) cc_final: 0.8729 (ppp) REVERT: J 1219 GLU cc_start: 0.8908 (pp20) cc_final: 0.8511 (pp20) REVERT: K 12 MET cc_start: 0.8960 (ppp) cc_final: 0.8578 (ppp) REVERT: K 52 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7549 (mm-30) REVERT: K 88 GLU cc_start: 0.7630 (tp30) cc_final: 0.6331 (pt0) outliers start: 96 outliers final: 56 residues processed: 311 average time/residue: 0.2419 time to fit residues: 130.2408 Evaluate side-chains 276 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 213 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 426 ARG Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 385 HIS Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 313 ASN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 800 VAL Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 1001 VAL Chi-restraints excluded: chain I residue 1006 HIS Chi-restraints excluded: chain I residue 1097 LEU Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 481 MET Chi-restraints excluded: chain J residue 527 MET Chi-restraints excluded: chain J residue 582 LEU Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 713 ILE Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1381 VAL Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 69 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 440 optimal weight: 0.6980 chunk 318 optimal weight: 1.9990 chunk 185 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 113 optimal weight: 50.0000 chunk 157 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 287 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** 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 = 0.3660 r_free = 0.3660 target = 0.059279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.043221 restraints weight = 303244.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.044455 restraints weight = 178741.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.045274 restraints weight = 126996.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.045816 restraints weight = 101081.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.046158 restraints weight = 86838.715| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 43482 Z= 0.171 Angle : 0.678 11.093 59185 Z= 0.334 Chirality : 0.043 0.210 6760 Planarity : 0.005 0.120 7415 Dihedral : 13.956 174.209 6870 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.61 % Rotamer: Outliers : 2.32 % Allowed : 15.12 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.12), residues: 5117 helix: 0.44 (0.12), residues: 1950 sheet: -0.67 (0.20), residues: 681 loop : -0.91 (0.13), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 276 TYR 0.026 0.001 TYR J1207 PHE 0.034 0.002 PHE F 307 TRP 0.036 0.002 TRP J 21 HIS 0.005 0.001 HIS I 999 Details of bonding type rmsd covalent geometry : bond 0.00379 (43464) covalent geometry : angle 0.67436 (59173) hydrogen bonds : bond 0.04223 ( 1802) hydrogen bonds : angle 5.51456 ( 5048) metal coordination : bond 0.00894 ( 8) metal coordination : angle 5.08462 ( 12) Misc. bond : bond 0.00143 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 223 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.8950 (ppp) cc_final: 0.8587 (ppp) REVERT: B 98 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7536 (m-80) REVERT: B 268 MET cc_start: 0.8816 (tpp) cc_final: 0.8469 (tpp) REVERT: B 340 GLU cc_start: 0.9441 (mm-30) cc_final: 0.9220 (pp20) REVERT: B 348 MET cc_start: 0.8229 (mmm) cc_final: 0.7022 (mmm) REVERT: B 405 MET cc_start: 0.8805 (ppp) cc_final: 0.8511 (ppp) REVERT: C 225 PHE cc_start: 0.9226 (t80) cc_final: 0.8550 (t80) REVERT: D 105 TYR cc_start: 0.9126 (t80) cc_final: 0.8657 (t80) REVERT: D 132 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8757 (t0) REVERT: D 277 LEU cc_start: 0.9581 (tp) cc_final: 0.9219 (mt) REVERT: D 387 MET cc_start: 0.7677 (ptt) cc_final: 0.6921 (ppp) REVERT: E 66 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7045 (tt) REVERT: E 225 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8898 (t80) REVERT: E 397 MET cc_start: 0.8296 (tmm) cc_final: 0.7996 (tmm) REVERT: F 348 MET cc_start: 0.7517 (mmm) cc_final: 0.7084 (mmm) REVERT: F 405 MET cc_start: 0.8546 (ppp) cc_final: 0.7990 (ppp) REVERT: G 1 MET cc_start: 0.7023 (ptp) cc_final: 0.6755 (mmt) REVERT: G 163 ASN cc_start: 0.8998 (t0) cc_final: 0.8601 (t0) REVERT: H 140 MET cc_start: 0.8351 (ppp) cc_final: 0.7363 (ppp) REVERT: I 99 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8683 (pp30) REVERT: I 340 MET cc_start: 0.8850 (tmm) cc_final: 0.8379 (tmm) REVERT: I 564 MET cc_start: 0.8714 (mpp) cc_final: 0.8115 (mpp) REVERT: I 880 MET cc_start: 0.8023 (mpp) cc_final: 0.7790 (mpp) REVERT: J 90 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8226 (tpp) REVERT: J 481 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8797 (tpp) REVERT: J 661 MET cc_start: 0.9151 (ppp) cc_final: 0.8714 (ppp) REVERT: J 1219 GLU cc_start: 0.8887 (pp20) cc_final: 0.8521 (pp20) REVERT: K 12 MET cc_start: 0.8986 (ppp) cc_final: 0.8767 (ppp) REVERT: K 52 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7652 (mm-30) REVERT: K 88 GLU cc_start: 0.7706 (tp30) cc_final: 0.6387 (pt0) REVERT: K 89 MET cc_start: 0.7057 (tpt) cc_final: 0.6697 (tpt) outliers start: 101 outliers final: 65 residues processed: 307 average time/residue: 0.2260 time to fit residues: 121.1251 Evaluate side-chains 289 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 217 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 385 HIS Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 313 ASN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 566 THR Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 1001 VAL Chi-restraints excluded: chain I residue 1006 HIS Chi-restraints excluded: chain I residue 1097 LEU Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 481 MET Chi-restraints excluded: chain J residue 527 MET Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 694 VAL Chi-restraints excluded: chain J residue 713 ILE Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1381 VAL Chi-restraints excluded: chain J residue 1421 LEU Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 69 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 237 optimal weight: 10.0000 chunk 479 optimal weight: 0.0020 chunk 453 optimal weight: 4.9990 chunk 465 optimal weight: 0.4980 chunk 125 optimal weight: 8.9990 chunk 411 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 314 optimal weight: 5.9990 chunk 302 optimal weight: 6.9990 chunk 325 optimal weight: 9.9990 chunk 513 optimal weight: 50.0000 overall best weight: 3.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 GLN ** J1364 HIS ** 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 = 0.3659 r_free = 0.3659 target = 0.059215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043195 restraints weight = 301700.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.044439 restraints weight = 177975.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.045223 restraints weight = 125825.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.045761 restraints weight = 100659.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.046125 restraints weight = 86603.253| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 43482 Z= 0.162 Angle : 0.671 11.112 59185 Z= 0.330 Chirality : 0.043 0.219 6760 Planarity : 0.005 0.119 7415 Dihedral : 13.868 171.968 6870 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 2.30 % Allowed : 16.11 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.12), residues: 5117 helix: 0.50 (0.12), residues: 1953 sheet: -0.65 (0.20), residues: 657 loop : -0.87 (0.13), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 426 TYR 0.025 0.001 TYR J1207 PHE 0.022 0.001 PHE D 419 TRP 0.029 0.001 TRP J 21 HIS 0.005 0.001 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00361 (43464) covalent geometry : angle 0.66748 (59173) hydrogen bonds : bond 0.04068 ( 1802) hydrogen bonds : angle 5.46211 ( 5048) metal coordination : bond 0.00829 ( 8) metal coordination : angle 4.84072 ( 12) Misc. bond : bond 0.00140 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 223 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8430 (t80) cc_final: 0.7508 (t80) REVERT: A 327 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8728 (mm) REVERT: A 405 MET cc_start: 0.8923 (ppp) cc_final: 0.8625 (ppp) REVERT: B 98 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: B 268 MET cc_start: 0.8834 (tpp) cc_final: 0.8463 (tpp) REVERT: B 348 MET cc_start: 0.8170 (mmm) cc_final: 0.6918 (mmm) REVERT: B 405 MET cc_start: 0.8818 (ppp) cc_final: 0.8570 (ppp) REVERT: C 225 PHE cc_start: 0.9175 (t80) cc_final: 0.8511 (t80) REVERT: C 397 MET cc_start: 0.7935 (ptm) cc_final: 0.7019 (tmm) REVERT: D 105 TYR cc_start: 0.9125 (t80) cc_final: 0.8660 (t80) REVERT: D 132 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8718 (t0) REVERT: D 277 LEU cc_start: 0.9555 (tp) cc_final: 0.9206 (mt) REVERT: D 387 MET cc_start: 0.7810 (ptt) cc_final: 0.6908 (ppp) REVERT: E 66 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7294 (tt) REVERT: E 100 LEU cc_start: 0.7862 (mt) cc_final: 0.7592 (mt) REVERT: E 225 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8886 (t80) REVERT: E 405 MET cc_start: 0.9571 (tmm) cc_final: 0.8888 (ppp) REVERT: F 97 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8824 (pm20) REVERT: F 348 MET cc_start: 0.7485 (mmm) cc_final: 0.7081 (mmm) REVERT: G 1 MET cc_start: 0.7017 (ptp) cc_final: 0.6773 (mmt) REVERT: G 5 LYS cc_start: 0.7170 (tptp) cc_final: 0.6154 (tppt) REVERT: G 163 ASN cc_start: 0.9019 (t0) cc_final: 0.8627 (t0) REVERT: H 140 MET cc_start: 0.8393 (ppp) cc_final: 0.7518 (ppp) REVERT: I 41 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7988 (p0) REVERT: I 99 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8733 (pp30) REVERT: I 340 MET cc_start: 0.8838 (tmm) cc_final: 0.8368 (tmm) REVERT: I 564 MET cc_start: 0.8741 (mpp) cc_final: 0.8096 (mpp) REVERT: I 880 MET cc_start: 0.8054 (mpp) cc_final: 0.7806 (mpp) REVERT: J 90 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8248 (tpp) REVERT: J 481 MET cc_start: 0.9061 (tpp) cc_final: 0.8771 (tpp) REVERT: J 661 MET cc_start: 0.9145 (ppp) cc_final: 0.8711 (ppp) REVERT: J 902 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8526 (pp) REVERT: J 1219 GLU cc_start: 0.8855 (pp20) cc_final: 0.8488 (pp20) REVERT: K 52 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7683 (mm-30) REVERT: K 88 GLU cc_start: 0.7725 (tp30) cc_final: 0.6379 (pt0) REVERT: K 89 MET cc_start: 0.6996 (tpt) cc_final: 0.6644 (tpt) outliers start: 100 outliers final: 71 residues processed: 304 average time/residue: 0.2411 time to fit residues: 128.5134 Evaluate side-chains 293 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 212 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 385 HIS Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 313 ASN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 566 THR Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 800 VAL Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 968 LEU Chi-restraints excluded: chain I residue 1001 VAL Chi-restraints excluded: chain I residue 1006 HIS Chi-restraints excluded: chain I residue 1097 LEU Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 527 MET Chi-restraints excluded: chain J residue 582 LEU Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 713 ILE Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1381 VAL Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1421 LEU Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 79 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 356 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 515 optimal weight: 10.0000 chunk 426 optimal weight: 0.9980 chunk 228 optimal weight: 2.9990 chunk 462 optimal weight: 5.9990 chunk 195 optimal weight: 0.0370 chunk 139 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 385 optimal weight: 0.0970 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1075 HIS J1364 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.060617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.044611 restraints weight = 299863.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.045901 restraints weight = 175729.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.046738 restraints weight = 123871.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.047298 restraints weight = 98220.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.047664 restraints weight = 84135.204| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 43482 Z= 0.123 Angle : 0.666 12.325 59185 Z= 0.326 Chirality : 0.043 0.354 6760 Planarity : 0.005 0.119 7415 Dihedral : 13.724 169.029 6870 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 1.82 % Allowed : 16.57 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.12), residues: 5117 helix: 0.53 (0.12), residues: 1955 sheet: -0.59 (0.20), residues: 659 loop : -0.82 (0.13), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 426 TYR 0.023 0.001 TYR J1207 PHE 0.022 0.001 PHE D 419 TRP 0.053 0.002 TRP J 21 HIS 0.005 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00273 (43464) covalent geometry : angle 0.66321 (59173) hydrogen bonds : bond 0.03771 ( 1802) hydrogen bonds : angle 5.29715 ( 5048) metal coordination : bond 0.00517 ( 8) metal coordination : angle 4.46308 ( 12) Misc. bond : bond 0.00132 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 228 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8383 (t80) cc_final: 0.7806 (t80) REVERT: A 327 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8717 (mm) REVERT: A 397 MET cc_start: 0.6620 (tmm) cc_final: 0.6096 (tmm) REVERT: A 405 MET cc_start: 0.8914 (ppp) cc_final: 0.8443 (ppp) REVERT: B 61 LEU cc_start: 0.9101 (tt) cc_final: 0.8742 (mm) REVERT: B 98 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7549 (m-80) REVERT: B 268 MET cc_start: 0.8867 (tpp) cc_final: 0.8490 (tpp) REVERT: B 348 MET cc_start: 0.8154 (mmm) cc_final: 0.7847 (tpp) REVERT: B 405 MET cc_start: 0.8809 (ppp) cc_final: 0.8584 (ppp) REVERT: C 225 PHE cc_start: 0.9167 (t80) cc_final: 0.8514 (t80) REVERT: C 397 MET cc_start: 0.7926 (ptm) cc_final: 0.7055 (tmm) REVERT: D 79 ASN cc_start: 0.8944 (t0) cc_final: 0.8612 (p0) REVERT: D 105 TYR cc_start: 0.9100 (t80) cc_final: 0.8676 (t80) REVERT: D 132 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8712 (t0) REVERT: D 313 ASN cc_start: 0.7102 (OUTLIER) cc_final: 0.6624 (t0) REVERT: D 387 MET cc_start: 0.7817 (ptt) cc_final: 0.6555 (ptt) REVERT: E 225 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8900 (t80) REVERT: E 405 MET cc_start: 0.9567 (tmm) cc_final: 0.8898 (ppp) REVERT: F 97 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8820 (pm20) REVERT: F 313 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7605 (t0) REVERT: G 1 MET cc_start: 0.7055 (ptp) cc_final: 0.6771 (mmt) REVERT: G 5 LYS cc_start: 0.7031 (tptp) cc_final: 0.6147 (tppt) REVERT: G 123 MET cc_start: 0.8462 (mmm) cc_final: 0.7920 (mpp) REVERT: G 163 ASN cc_start: 0.9035 (t0) cc_final: 0.8666 (t0) REVERT: H 140 MET cc_start: 0.8393 (ppp) cc_final: 0.7564 (ppp) REVERT: I 99 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.7998 (pp30) REVERT: I 340 MET cc_start: 0.8869 (tmm) cc_final: 0.8371 (tmm) REVERT: I 564 MET cc_start: 0.8657 (mpp) cc_final: 0.8127 (mpp) REVERT: I 1031 ARG cc_start: 0.8000 (mpt180) cc_final: 0.7672 (mmt180) REVERT: J 90 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8104 (tpp) REVERT: J 481 MET cc_start: 0.9052 (tpp) cc_final: 0.8741 (tpp) REVERT: J 661 MET cc_start: 0.9160 (ppp) cc_final: 0.8660 (ppp) REVERT: J 902 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8506 (pp) REVERT: J 1219 GLU cc_start: 0.8819 (pp20) cc_final: 0.8455 (pp20) REVERT: K 52 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7448 (mm-30) REVERT: K 88 GLU cc_start: 0.7677 (tp30) cc_final: 0.6248 (pt0) REVERT: K 89 MET cc_start: 0.7052 (tpt) cc_final: 0.6728 (tpt) outliers start: 79 outliers final: 53 residues processed: 297 average time/residue: 0.2361 time to fit residues: 122.4343 Evaluate side-chains 280 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 217 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 385 HIS Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 313 ASN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 566 THR Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 1001 VAL Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 527 MET Chi-restraints excluded: chain J residue 619 LEU Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 694 VAL Chi-restraints excluded: chain J residue 713 ILE Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 79 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 29 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 476 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 218 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 516 optimal weight: 10.0000 chunk 5 optimal weight: 40.0000 chunk 269 optimal weight: 7.9990 chunk 305 optimal weight: 0.5980 chunk 266 optimal weight: 10.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1037 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.058502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.042488 restraints weight = 303302.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.043686 restraints weight = 180766.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.044459 restraints weight = 129145.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.044963 restraints weight = 103768.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.045290 restraints weight = 90078.267| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 43482 Z= 0.212 Angle : 0.716 13.494 59185 Z= 0.352 Chirality : 0.044 0.235 6760 Planarity : 0.005 0.118 7415 Dihedral : 13.736 163.738 6870 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.29 % Favored : 93.63 % Rotamer: Outliers : 1.93 % Allowed : 16.93 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.12), residues: 5117 helix: 0.48 (0.12), residues: 1973 sheet: -0.67 (0.20), residues: 674 loop : -0.88 (0.13), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 426 TYR 0.028 0.002 TYR J 868 PHE 0.023 0.002 PHE I1032 TRP 0.063 0.002 TRP J 21 HIS 0.007 0.001 HIS I 999 Details of bonding type rmsd covalent geometry : bond 0.00465 (43464) covalent geometry : angle 0.71302 (59173) hydrogen bonds : bond 0.04276 ( 1802) hydrogen bonds : angle 5.41474 ( 5048) metal coordination : bond 0.01132 ( 8) metal coordination : angle 4.74610 ( 12) Misc. bond : bond 0.00132 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 212 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8385 (t80) cc_final: 0.7782 (t80) REVERT: A 327 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8821 (mm) REVERT: A 397 MET cc_start: 0.6683 (tmm) cc_final: 0.6180 (tmm) REVERT: A 405 MET cc_start: 0.8912 (ppp) cc_final: 0.8411 (ppp) REVERT: B 98 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7560 (m-80) REVERT: B 268 MET cc_start: 0.8861 (tpp) cc_final: 0.8597 (tpp) REVERT: B 348 MET cc_start: 0.8132 (mmm) cc_final: 0.6798 (mmm) REVERT: B 405 MET cc_start: 0.8862 (ppp) cc_final: 0.8624 (ppp) REVERT: C 225 PHE cc_start: 0.9182 (t80) cc_final: 0.8513 (t80) REVERT: C 397 MET cc_start: 0.7924 (ptm) cc_final: 0.7312 (tmm) REVERT: D 105 TYR cc_start: 0.9084 (t80) cc_final: 0.8626 (t80) REVERT: D 132 ASP cc_start: 0.8996 (OUTLIER) cc_final: 0.8699 (t0) REVERT: D 387 MET cc_start: 0.7900 (ptt) cc_final: 0.6526 (ptt) REVERT: E 225 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8910 (t80) REVERT: E 405 MET cc_start: 0.9562 (tmm) cc_final: 0.8916 (ppp) REVERT: F 97 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8858 (pm20) REVERT: F 348 MET cc_start: 0.7732 (mmm) cc_final: 0.6097 (mmm) REVERT: G 1 MET cc_start: 0.7085 (ptp) cc_final: 0.6804 (mmt) REVERT: G 5 LYS cc_start: 0.6927 (tptp) cc_final: 0.5791 (tppt) REVERT: G 163 ASN cc_start: 0.9047 (t0) cc_final: 0.8695 (t0) REVERT: H 140 MET cc_start: 0.8495 (ppp) cc_final: 0.7642 (ppp) REVERT: I 340 MET cc_start: 0.8837 (tmm) cc_final: 0.8382 (tmm) REVERT: I 564 MET cc_start: 0.8840 (mpp) cc_final: 0.8232 (mpp) REVERT: J 90 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8245 (tpp) REVERT: J 481 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8705 (tpp) REVERT: J 661 MET cc_start: 0.9098 (ppp) cc_final: 0.8629 (ppp) REVERT: J 902 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8518 (pp) REVERT: J 1219 GLU cc_start: 0.8901 (pp20) cc_final: 0.8542 (pp20) REVERT: K 52 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7717 (mm-30) REVERT: K 54 LEU cc_start: 0.3219 (OUTLIER) cc_final: 0.2884 (mt) REVERT: K 88 GLU cc_start: 0.7899 (tp30) cc_final: 0.6410 (pt0) REVERT: K 89 MET cc_start: 0.7075 (tpt) cc_final: 0.6745 (tpt) outliers start: 84 outliers final: 62 residues processed: 282 average time/residue: 0.2346 time to fit residues: 115.4998 Evaluate side-chains 276 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 205 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 385 HIS Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 313 ASN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 566 THR Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 800 VAL Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 868 ASP Chi-restraints excluded: chain I residue 999 HIS Chi-restraints excluded: chain I residue 1001 VAL Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 481 MET Chi-restraints excluded: chain J residue 527 MET Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 694 VAL Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 1044 LEU Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1381 VAL Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1421 LEU Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 268 optimal weight: 3.9990 chunk 316 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 507 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 350 optimal weight: 8.9990 chunk 497 optimal weight: 2.9990 chunk 474 optimal weight: 0.5980 chunk 513 optimal weight: 50.0000 chunk 11 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1047 HIS I1107 ASN J1037 GLN ** J1393 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 = 0.3673 r_free = 0.3673 target = 0.059704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.043639 restraints weight = 297614.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.044883 restraints weight = 176494.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.045706 restraints weight = 125712.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.046252 restraints weight = 99907.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.046626 restraints weight = 85876.104| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 43482 Z= 0.133 Angle : 0.684 13.211 59185 Z= 0.332 Chirality : 0.044 0.255 6760 Planarity : 0.005 0.118 7415 Dihedral : 13.669 164.028 6870 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.78 % Favored : 94.12 % Rotamer: Outliers : 1.77 % Allowed : 17.21 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.12), residues: 5117 helix: 0.59 (0.12), residues: 1959 sheet: -0.65 (0.20), residues: 631 loop : -0.84 (0.13), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 333 TYR 0.031 0.001 TYR J 868 PHE 0.021 0.001 PHE D 419 TRP 0.057 0.002 TRP J 21 HIS 0.007 0.001 HIS I 999 Details of bonding type rmsd covalent geometry : bond 0.00298 (43464) covalent geometry : angle 0.68094 (59173) hydrogen bonds : bond 0.03791 ( 1802) hydrogen bonds : angle 5.29583 ( 5048) metal coordination : bond 0.00590 ( 8) metal coordination : angle 4.46288 ( 12) Misc. bond : bond 0.00123 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10234 Ramachandran restraints generated. 5117 Oldfield, 0 Emsley, 5117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 213 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8353 (t80) cc_final: 0.7735 (t80) REVERT: A 327 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8788 (mm) REVERT: A 397 MET cc_start: 0.6635 (tmm) cc_final: 0.6159 (tmm) REVERT: A 405 MET cc_start: 0.8891 (ppp) cc_final: 0.8396 (ppp) REVERT: B 98 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: B 268 MET cc_start: 0.8846 (tpp) cc_final: 0.8529 (tpp) REVERT: B 348 MET cc_start: 0.8090 (mmm) cc_final: 0.7831 (tpp) REVERT: C 225 PHE cc_start: 0.9152 (t80) cc_final: 0.8494 (t80) REVERT: C 397 MET cc_start: 0.8114 (ptm) cc_final: 0.6921 (tmm) REVERT: D 79 ASN cc_start: 0.8958 (t0) cc_final: 0.8626 (p0) REVERT: D 105 TYR cc_start: 0.9055 (t80) cc_final: 0.8638 (t80) REVERT: D 132 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8695 (t0) REVERT: D 313 ASN cc_start: 0.7217 (OUTLIER) cc_final: 0.6750 (t0) REVERT: D 387 MET cc_start: 0.7848 (ptt) cc_final: 0.6542 (ptt) REVERT: E 225 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8902 (t80) REVERT: E 288 THR cc_start: 0.7400 (OUTLIER) cc_final: 0.7038 (p) REVERT: F 97 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8852 (pm20) REVERT: F 348 MET cc_start: 0.7502 (mmm) cc_final: 0.5928 (mmm) REVERT: G 1 MET cc_start: 0.7059 (ptp) cc_final: 0.6783 (mmt) REVERT: G 5 LYS cc_start: 0.6981 (tptp) cc_final: 0.6050 (tppt) REVERT: G 123 MET cc_start: 0.8445 (mmm) cc_final: 0.7978 (mpp) REVERT: G 163 ASN cc_start: 0.9068 (t0) cc_final: 0.8691 (t0) REVERT: H 140 MET cc_start: 0.8602 (ppp) cc_final: 0.7806 (ppp) REVERT: I 99 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8809 (pp30) REVERT: I 340 MET cc_start: 0.8857 (tmm) cc_final: 0.8376 (tmm) REVERT: I 1031 ARG cc_start: 0.8080 (mpt180) cc_final: 0.7755 (mmt180) REVERT: J 90 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8159 (tpp) REVERT: J 481 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8644 (tpp) REVERT: J 527 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7957 (mtt) REVERT: J 661 MET cc_start: 0.9121 (ppp) cc_final: 0.8624 (ppp) REVERT: J 902 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8500 (pp) REVERT: J 1219 GLU cc_start: 0.8848 (pp20) cc_final: 0.8477 (pp20) REVERT: K 52 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7677 (mm-30) REVERT: K 88 GLU cc_start: 0.7870 (tp30) cc_final: 0.6437 (pt0) REVERT: K 89 MET cc_start: 0.7058 (tpt) cc_final: 0.6787 (tpt) outliers start: 77 outliers final: 57 residues processed: 280 average time/residue: 0.2341 time to fit residues: 115.0441 Evaluate side-chains 279 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 210 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 385 HIS Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 404 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 313 ASN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 566 THR Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 800 VAL Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 1001 VAL Chi-restraints excluded: chain I residue 1106 ASP Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 481 MET Chi-restraints excluded: chain J residue 527 MET Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 694 VAL Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 1044 LEU Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 40 optimal weight: 0.0670 chunk 146 optimal weight: 1.9990 chunk 367 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 422 optimal weight: 3.9990 chunk 357 optimal weight: 0.9990 chunk 344 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 381 optimal weight: 1.9990 chunk 373 optimal weight: 2.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1107 ASN ** J1393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.059978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.043941 restraints weight = 301354.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.045225 restraints weight = 176571.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046043 restraints weight = 124657.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.046571 restraints weight = 99051.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.046939 restraints weight = 85241.405| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 43482 Z= 0.128 Angle : 0.674 12.645 59185 Z= 0.327 Chirality : 0.043 0.269 6760 Planarity : 0.005 0.117 7415 Dihedral : 13.563 158.326 6870 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 1.61 % Allowed : 17.44 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.12), residues: 5117 helix: 0.66 (0.12), residues: 1960 sheet: -0.65 (0.20), residues: 668 loop : -0.81 (0.13), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 276 TYR 0.032 0.001 TYR J 868 PHE 0.021 0.001 PHE D 419 TRP 0.054 0.002 TRP J 21 HIS 0.014 0.001 HIS C 351 Details of bonding type rmsd covalent geometry : bond 0.00287 (43464) covalent geometry : angle 0.67098 (59173) hydrogen bonds : bond 0.03669 ( 1802) hydrogen bonds : angle 5.17636 ( 5048) metal coordination : bond 0.00575 ( 8) metal coordination : angle 4.22189 ( 12) Misc. bond : bond 0.00117 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8086.26 seconds wall clock time: 140 minutes 35.53 seconds (8435.53 seconds total)