Starting phenix.real_space_refine on Tue Jul 7 02:57:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hsr_35004/07_2026/8hsr_35004.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hsr_35004/07_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_35004/07_2026/8hsr_35004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hsr_35004/07_2026/8hsr_35004.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hsr_35004/07_2026/8hsr_35004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hsr_35004/07_2026/8hsr_35004.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hsr_35004/07_2026/8hsr_35004.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hsr_35004/07_2026/8hsr_35004.cif" } 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-6108/lib/python3.11/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: 102 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: 8.87, per 1000 atoms: 0.21 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: 3.89 Conformation dependent library (CDL) restraints added in 1.7 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: 5.36 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: 12.27 Time building geometry restraints manager: 5.15 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=" C5' DA T 22 " pdb=" C4' DA T 22 " ideal model delta sigma weight residual 1.512 1.548 -0.036 7.00e-03 2.04e+04 2.63e+01 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 ... (remaining 43459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 58300 2.76 - 5.52: 770 5.52 - 8.29: 79 8.29 - 11.05: 15 11.05 - 13.81: 9 Bond angle restraints: 59173 Sorted by residual: angle pdb=" O5' DA T 22 " pdb=" C5' DA T 22 " pdb=" C4' DA T 22 " ideal model delta sigma weight residual 109.40 114.79 -5.39 8.00e-01 1.56e+00 4.54e+01 angle pdb=" O4' DA T 22 " pdb=" C4' DA T 22 " pdb=" C3' DA T 22 " ideal model delta sigma weight residual 106.00 102.37 3.63 6.00e-01 2.78e+00 3.67e+01 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=" O4' DG T 23 " pdb=" C4' DG T 23 " pdb=" C3' DG T 23 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.35e+01 ... (remaining 59168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 26002 35.65 - 71.30: 560 71.30 - 106.96: 35 106.96 - 142.61: 2 142.61 - 178.26: 5 Dihedral angle restraints: 26604 sinusoidal: 11828 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 26601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 5564 0.061 - 0.123: 1097 0.123 - 0.184: 90 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=" 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 2.34 -2.62 -0.28 2.00e-01 2.50e+01 1.98e+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 ... (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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.780 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 50.150 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5401 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= 0.437 Angle : 0.819 13.809 59185 Z= 0.447 Chirality : 0.047 0.307 6760 Planarity : 0.006 0.128 7415 Dihedral : 14.948 178.259 17078 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/Z covalent geometry : bond 0.00502 / 0.27 (43464) covalent geometry : angle 0.81221 / 0.45 (59173) hydrogen bonds : bond 0.18457 / 12.69 ( 1802) hydrogen bonds : angle 7.48166 / 5.24 ( 5048) metal coordination : bond 0.01411 / 0.71 ( 8) metal coordination : angle 7.60002 / 5.70 ( 12) Misc. bond : bond 0.22732 / 12.07 ( 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 : 1.701 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: 0.2559 time to fit residues: 138.8941 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 : 1.721 ------------------------------------------------------------------------------- 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: 40.0000 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN B 97 GLN ** 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 254 HIS ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 HIS G 212 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.061778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.045621 restraints weight = 300874.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.046923 restraints weight = 177760.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.047775 restraints weight = 125454.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.048340 restraints weight = 99290.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.048694 restraints weight = 84956.930| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 43482 Z= 0.182 Angle : 0.768 12.854 59185 Z= 0.385 Chirality : 0.047 0.212 6760 Planarity : 0.007 0.123 7415 Dihedral : 14.038 171.333 6806 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.41 % Favored : 93.49 % Rotamer: Outliers : 0.85 % Allowed : 7.65 % Favored : 91.50 % 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: -0.80 (0.12), residues: 5117 helix: 0.14 (0.12), residues: 1939 sheet: -0.66 (0.19), residues: 712 loop : -0.97 (0.13), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 276 TYR 0.028 0.002 TYR J1207 PHE 0.028 0.002 PHE F 362 TRP 0.017 0.002 TRP J 21 HIS 0.007 0.001 HIS E 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (43464) covalent geometry : angle 0.76209 / 0.38 (59173) hydrogen bonds : bond 0.05645 / 3.85 ( 1802) hydrogen bonds : angle 6.20808 / 4.38 ( 5048) metal coordination : bond 0.01114 / 0.58 ( 8) metal coordination : angle 6.53576 / 4.92 ( 12) Misc. bond : bond 0.00654 / 0.37 ( 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 292 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 1.648 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: A 134 GLU cc_start: 0.9339 (mp0) cc_final: 0.8823 (mp0) REVERT: A 397 MET cc_start: 0.6735 (tmm) cc_final: 0.6383 (tmm) REVERT: A 405 MET cc_start: 0.8783 (ppp) cc_final: 0.8459 (ppp) REVERT: B 268 MET cc_start: 0.8689 (tpp) cc_final: 0.8377 (tpp) REVERT: C 105 TYR cc_start: 0.7737 (t80) cc_final: 0.7398 (t80) REVERT: C 397 MET cc_start: 0.7838 (ttt) cc_final: 0.6890 (ptm) REVERT: D 268 MET cc_start: 0.7767 (mmp) cc_final: 0.7532 (mmp) REVERT: D 387 MET cc_start: 0.7841 (ptt) cc_final: 0.6933 (ppp) REVERT: E 225 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8832 (t80) REVERT: E 405 MET cc_start: 0.9436 (tmm) cc_final: 0.8960 (ppp) REVERT: G 1 MET cc_start: 0.6904 (ptp) cc_final: 0.6691 (mmt) REVERT: G 163 ASN cc_start: 0.8770 (t0) cc_final: 0.8356 (t0) REVERT: I 229 MET cc_start: 0.7133 (mpp) cc_final: 0.6868 (mmm) REVERT: I 340 MET cc_start: 0.8824 (tmm) cc_final: 0.8323 (tmm) REVERT: I 880 MET cc_start: 0.8108 (mpp) cc_final: 0.7877 (mpp) REVERT: I 1031 ARG cc_start: 0.7789 (mpt180) cc_final: 0.7479 (mmt180) REVERT: I 1035 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8365 (mtt) REVERT: J 661 MET cc_start: 0.9289 (ppp) cc_final: 0.8833 (ppp) REVERT: J 1219 GLU cc_start: 0.8856 (pp20) cc_final: 0.8418 (pp20) REVERT: K 29 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8664 (mp10) REVERT: K 52 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7676 (mm-30) outliers start: 37 outliers final: 19 residues processed: 277 average time/residue: 0.2436 time to fit residues: 116.3386 Evaluate side-chains 237 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE 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 D residue 385 HIS Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 283 LEU 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 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 Chi-restraints excluded: chain K residue 29 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 369 optimal weight: 10.0000 chunk 491 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 240 optimal weight: 9.9990 chunk 417 optimal weight: 1.9990 chunk 375 optimal weight: 9.9990 chunk 305 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 350 optimal weight: 9.9990 chunk 401 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 ASN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.061571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.045342 restraints weight = 300112.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.046617 restraints weight = 178076.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.047475 restraints weight = 126283.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.048026 restraints weight = 100088.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.048388 restraints weight = 86183.931| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 43482 Z= 0.165 Angle : 0.705 12.601 59185 Z= 0.351 Chirality : 0.045 0.191 6760 Planarity : 0.006 0.122 7415 Dihedral : 13.944 179.619 6806 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.55 % Favored : 93.38 % Rotamer: Outliers : 0.94 % Allowed : 10.55 % Favored : 88.51 % 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: -0.75 (0.12), residues: 5117 helix: 0.21 (0.12), residues: 1940 sheet: -0.72 (0.18), residues: 742 loop : -0.92 (0.13), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 276 TYR 0.027 0.001 TYR J1207 PHE 0.025 0.002 PHE F 362 TRP 0.017 0.001 TRP J 21 HIS 0.013 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (43464) covalent geometry : angle 0.69961 / 0.35 (59173) hydrogen bonds : bond 0.05078 / 3.48 ( 1802) hydrogen bonds : angle 5.96578 / 4.21 ( 5048) metal coordination : bond 0.00917 / 0.49 ( 8) metal coordination : angle 6.09222 / 4.53 ( 12) Misc. bond : bond 0.00361 / 0.23 ( 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 277 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 1.518 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: A 134 GLU cc_start: 0.9175 (mp0) cc_final: 0.8805 (mp0) REVERT: A 397 MET cc_start: 0.6788 (tmm) cc_final: 0.6400 (tmm) REVERT: A 405 MET cc_start: 0.8766 (ppp) cc_final: 0.8380 (ppp) REVERT: B 348 MET cc_start: 0.7475 (mmm) cc_final: 0.6444 (mmm) REVERT: B 397 MET cc_start: 0.6999 (pmm) cc_final: 0.6535 (pmm) REVERT: B 403 MET cc_start: 0.8791 (mmm) cc_final: 0.8589 (mmm) REVERT: B 405 MET cc_start: 0.8776 (ppp) cc_final: 0.8554 (ppp) REVERT: C 105 TYR cc_start: 0.7759 (t80) cc_final: 0.7479 (t80) REVERT: C 397 MET cc_start: 0.7916 (ttt) cc_final: 0.7177 (ptm) REVERT: D 387 MET cc_start: 0.7631 (ptt) cc_final: 0.6713 (ppp) REVERT: E 225 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8880 (t80) REVERT: E 348 MET cc_start: 0.7722 (mmm) cc_final: 0.6930 (mpp) REVERT: F 403 MET cc_start: 0.9199 (tmm) cc_final: 0.8649 (tmm) REVERT: G 1 MET cc_start: 0.6866 (ptp) cc_final: 0.6651 (mmt) REVERT: G 163 ASN cc_start: 0.8820 (t0) cc_final: 0.8490 (t0) REVERT: I 340 MET cc_start: 0.8789 (tmm) cc_final: 0.8301 (tmm) REVERT: I 880 MET cc_start: 0.8088 (mpp) cc_final: 0.7856 (mpp) REVERT: I 1031 ARG cc_start: 0.7811 (mpt180) cc_final: 0.7423 (tpp-160) REVERT: J 481 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8763 (tpp) REVERT: J 573 MET cc_start: 0.9293 (mtm) cc_final: 0.9068 (mtm) REVERT: J 661 MET cc_start: 0.9253 (ppp) cc_final: 0.8814 (ppp) REVERT: J 980 MET cc_start: 0.8381 (mmt) cc_final: 0.8141 (mmt) REVERT: J 1219 GLU cc_start: 0.8839 (pp20) cc_final: 0.8415 (pp20) REVERT: K 88 GLU cc_start: 0.7132 (tp30) cc_final: 0.5836 (pt0) outliers start: 41 outliers final: 23 residues processed: 264 average time/residue: 0.2316 time to fit residues: 105.1123 Evaluate side-chains 238 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL 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 255 GLU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 288 THR 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 637 LEU Chi-restraints excluded: chain I residue 905 ILE 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 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: 9.9990 chunk 78 optimal weight: 20.0000 chunk 258 optimal weight: 9.9990 chunk 447 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 465 optimal weight: 0.0040 chunk 293 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 421 optimal weight: 6.9990 chunk 441 optimal weight: 8.9990 overall best weight: 6.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 97 GLN ** 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 138 ASN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 GLN ** 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** ** 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 = 0.3664 r_free = 0.3664 target = 0.059587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.043534 restraints weight = 305058.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.044803 restraints weight = 182181.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.045581 restraints weight = 129131.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.046099 restraints weight = 103470.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.046425 restraints weight = 89570.982| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 43482 Z= 0.255 Angle : 0.746 11.851 59185 Z= 0.374 Chirality : 0.045 0.211 6760 Planarity : 0.006 0.122 7415 Dihedral : 13.935 176.889 6806 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.21 % Favored : 92.71 % Rotamer: Outliers : 1.63 % Allowed : 12.50 % Favored : 85.87 % 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: -0.81 (0.12), residues: 5117 helix: 0.18 (0.11), residues: 1955 sheet: -0.75 (0.19), residues: 722 loop : -0.99 (0.13), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 276 TYR 0.030 0.002 TYR J1207 PHE 0.027 0.002 PHE F 362 TRP 0.022 0.002 TRP J 21 HIS 0.008 0.001 HIS I1047 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.26 (43464) covalent geometry : angle 0.74109 / 0.37 (59173) hydrogen bonds : bond 0.05137 / 3.54 ( 1802) hydrogen bonds : angle 5.96333 / 4.20 ( 5048) metal coordination : bond 0.01458 / 0.82 ( 8) metal coordination : angle 6.08034 / 4.57 ( 12) Misc. bond : bond 0.00163 / 0.10 ( 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 291 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 220 time to evaluate : 1.684 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: A 405 MET cc_start: 0.8787 (ppp) cc_final: 0.8360 (ppp) REVERT: B 132 ASP cc_start: 0.8883 (p0) cc_final: 0.8672 (p0) REVERT: B 338 ILE cc_start: 0.9266 (mt) cc_final: 0.9020 (pt) REVERT: B 348 MET cc_start: 0.7808 (mmm) cc_final: 0.6883 (mmm) REVERT: B 397 MET cc_start: 0.7058 (pmm) cc_final: 0.6560 (pmm) REVERT: B 405 MET cc_start: 0.8793 (ppp) cc_final: 0.8484 (ppp) REVERT: C 105 TYR cc_start: 0.7886 (t80) cc_final: 0.7659 (t80) REVERT: C 348 MET cc_start: 0.8225 (mmm) cc_final: 0.7266 (mmm) REVERT: D 132 ASP cc_start: 0.9028 (OUTLIER) cc_final: 0.8744 (t0) REVERT: D 277 LEU cc_start: 0.9564 (tp) cc_final: 0.9206 (mt) REVERT: D 387 MET cc_start: 0.7773 (ptt) cc_final: 0.6910 (ppp) REVERT: D 403 MET cc_start: 0.9534 (OUTLIER) cc_final: 0.9199 (mpp) REVERT: E 66 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.6314 (tt) REVERT: E 225 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8951 (t80) REVERT: E 348 MET cc_start: 0.7874 (mmm) cc_final: 0.6867 (mpp) REVERT: E 405 MET cc_start: 0.9597 (tmm) cc_final: 0.9030 (ppp) REVERT: F 348 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7239 (mmm) REVERT: G 1 MET cc_start: 0.6950 (ptp) cc_final: 0.6728 (mmt) REVERT: G 163 ASN cc_start: 0.8894 (t0) cc_final: 0.8637 (t0) REVERT: H 140 MET cc_start: 0.8178 (ppp) cc_final: 0.6891 (ppp) REVERT: I 340 MET cc_start: 0.8859 (tmm) cc_final: 0.8396 (tmm) REVERT: I 880 MET cc_start: 0.8170 (mpp) cc_final: 0.7937 (mpp) REVERT: J 456 MET cc_start: 0.3638 (ttp) cc_final: 0.2741 (ttp) REVERT: J 481 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8791 (tpp) REVERT: J 661 MET cc_start: 0.9182 (ppp) cc_final: 0.8767 (ppp) REVERT: J 980 MET cc_start: 0.8480 (mmt) cc_final: 0.8261 (mmm) REVERT: J 1219 GLU cc_start: 0.8889 (pp20) cc_final: 0.8432 (pp20) REVERT: K 88 GLU cc_start: 0.7332 (tp30) cc_final: 0.6031 (pt0) outliers start: 71 outliers final: 44 residues processed: 273 average time/residue: 0.2307 time to fit residues: 110.0503 Evaluate side-chains 259 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 1.939 ------------------------------------------------------------------------------- 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 171 LEU Chi-restraints excluded: chain B residue 191 THR 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 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 D residue 338 ILE 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 66 LEU Chi-restraints excluded: chain E residue 97 GLN 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 283 LEU Chi-restraints excluded: chain E residue 288 THR 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 F residue 348 MET 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 H residue 142 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 182 VAL 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 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 Chi-restraints excluded: chain K residue 47 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 134 optimal weight: 20.0000 chunk 410 optimal weight: 1.9990 chunk 295 optimal weight: 5.9990 chunk 504 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 485 optimal weight: 8.9990 chunk 461 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 351 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS ** 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** ** F 97 GLN ** 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** J 909 ASN J1334 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 = 0.3679 r_free = 0.3679 target = 0.060152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.044032 restraints weight = 304011.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.045280 restraints weight = 179547.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.046082 restraints weight = 127847.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.046618 restraints weight = 102433.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.046968 restraints weight = 88342.505| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 43482 Z= 0.172 Angle : 0.693 11.034 59185 Z= 0.344 Chirality : 0.044 0.217 6760 Planarity : 0.005 0.121 7415 Dihedral : 13.839 179.777 6806 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.53 % Favored : 93.39 % Rotamer: Outliers : 1.63 % Allowed : 13.74 % Favored : 84.63 % 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: -0.72 (0.12), residues: 5117 helix: 0.28 (0.12), residues: 1955 sheet: -0.71 (0.19), residues: 699 loop : -0.96 (0.13), residues: 2463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 276 TYR 0.028 0.001 TYR J1207 PHE 0.021 0.002 PHE F 362 TRP 0.028 0.002 TRP J 21 HIS 0.005 0.001 HIS J1103 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (43464) covalent geometry : angle 0.68797 / 0.34 (59173) hydrogen bonds : bond 0.04601 / 3.14 ( 1802) hydrogen bonds : angle 5.78068 / 4.07 ( 5048) metal coordination : bond 0.00924 / 0.52 ( 8) metal coordination : angle 5.61670 / 4.27 ( 12) Misc. bond : bond 0.00142 / 0.10 ( 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 295 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 224 time to evaluate : 1.586 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: A 405 MET cc_start: 0.8787 (ppp) cc_final: 0.8451 (ppp) REVERT: B 268 MET cc_start: 0.8715 (tpp) cc_final: 0.8286 (tpp) REVERT: B 338 ILE cc_start: 0.9258 (mt) cc_final: 0.9001 (pt) REVERT: B 348 MET cc_start: 0.8008 (mmm) cc_final: 0.6917 (mmm) REVERT: B 397 MET cc_start: 0.7105 (pmm) cc_final: 0.6751 (pmm) REVERT: B 403 MET cc_start: 0.8819 (mmm) cc_final: 0.8577 (mmm) REVERT: B 405 MET cc_start: 0.8778 (ppp) cc_final: 0.8430 (ppp) REVERT: C 348 MET cc_start: 0.8214 (mmm) cc_final: 0.7483 (mmm) REVERT: D 132 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8765 (t0) REVERT: D 387 MET cc_start: 0.7845 (ptt) cc_final: 0.6940 (ppp) REVERT: E 66 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.6627 (tt) REVERT: E 225 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8884 (t80) REVERT: E 348 MET cc_start: 0.7862 (mmm) cc_final: 0.7044 (mpp) REVERT: E 405 MET cc_start: 0.9583 (tmm) cc_final: 0.9098 (ppp) REVERT: F 348 MET cc_start: 0.7870 (tpt) cc_final: 0.7142 (mmm) REVERT: G 163 ASN cc_start: 0.8938 (t0) cc_final: 0.8677 (t0) REVERT: H 140 MET cc_start: 0.8126 (ppp) cc_final: 0.6910 (ppp) REVERT: I 99 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8705 (pp30) REVERT: I 340 MET cc_start: 0.8812 (tmm) cc_final: 0.8342 (tmm) REVERT: I 564 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8300 (mpp) REVERT: I 880 MET cc_start: 0.8105 (mpp) cc_final: 0.7855 (mpp) REVERT: J 456 MET cc_start: 0.3610 (ttp) cc_final: 0.2735 (ttp) REVERT: J 481 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8812 (tpp) REVERT: J 661 MET cc_start: 0.9158 (ppp) cc_final: 0.8720 (ppp) REVERT: J 980 MET cc_start: 0.8556 (mmt) cc_final: 0.8330 (mmt) REVERT: J 1219 GLU cc_start: 0.8850 (pp20) cc_final: 0.8452 (pp20) REVERT: K 52 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7532 (mm-30) REVERT: K 88 GLU cc_start: 0.7430 (tp30) cc_final: 0.6214 (pt0) outliers start: 71 outliers final: 42 residues processed: 277 average time/residue: 0.2140 time to fit residues: 104.2877 Evaluate side-chains 261 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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 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 274 ILE 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 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 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 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 196 THR Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 564 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 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 J residue 829 VAL Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 47 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 440 optimal weight: 7.9990 chunk 318 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 113 optimal weight: 50.0000 chunk 157 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 287 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 245 ASN ** 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 97 GLN ** 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** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.060606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.044462 restraints weight = 299463.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.045747 restraints weight = 175142.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.046584 restraints weight = 123509.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.047138 restraints weight = 97928.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.047492 restraints weight = 84286.662| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 43482 Z= 0.138 Angle : 0.675 14.903 59185 Z= 0.333 Chirality : 0.044 0.219 6760 Planarity : 0.005 0.121 7415 Dihedral : 13.703 178.354 6806 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.33 % Favored : 93.59 % Rotamer: Outliers : 1.68 % Allowed : 15.00 % Favored : 83.32 % 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: -0.60 (0.12), residues: 5117 helix: 0.40 (0.12), residues: 1952 sheet: -0.68 (0.19), residues: 696 loop : -0.90 (0.13), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 276 TYR 0.026 0.001 TYR J1207 PHE 0.022 0.001 PHE D 419 TRP 0.037 0.002 TRP J 21 HIS 0.005 0.001 HIS J1103 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (43464) covalent geometry : angle 0.67118 / 0.33 (59173) hydrogen bonds : bond 0.04277 / 2.90 ( 1802) hydrogen bonds : angle 5.57730 / 3.94 ( 5048) metal coordination : bond 0.00720 / 0.39 ( 8) metal coordination : angle 5.12964 / 3.86 ( 12) Misc. bond : bond 0.00133 / 0.09 ( 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 301 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 228 time to evaluate : 1.715 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: A 405 MET cc_start: 0.8882 (ppp) cc_final: 0.8545 (ppp) REVERT: B 61 LEU cc_start: 0.9025 (tt) cc_final: 0.8672 (mm) REVERT: B 268 MET cc_start: 0.8808 (tpp) cc_final: 0.8473 (tpp) REVERT: B 348 MET cc_start: 0.8014 (mmm) cc_final: 0.6903 (mmm) REVERT: B 405 MET cc_start: 0.8842 (ppp) cc_final: 0.8543 (ppp) REVERT: C 225 PHE cc_start: 0.9263 (t80) cc_final: 0.8661 (t80) REVERT: C 348 MET cc_start: 0.8315 (mmm) cc_final: 0.7602 (mmm) REVERT: D 105 TYR cc_start: 0.9183 (t80) cc_final: 0.8727 (t80) REVERT: D 132 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8749 (t0) REVERT: D 277 LEU cc_start: 0.9558 (tp) cc_final: 0.9185 (mt) REVERT: D 387 MET cc_start: 0.7831 (ptt) cc_final: 0.7044 (ppp) REVERT: E 66 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.6555 (tt) REVERT: E 225 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8900 (t80) REVERT: E 348 MET cc_start: 0.7747 (mmm) cc_final: 0.7205 (mpp) REVERT: E 405 MET cc_start: 0.9587 (tmm) cc_final: 0.9275 (ppp) REVERT: F 348 MET cc_start: 0.7749 (tpt) cc_final: 0.7183 (mmm) REVERT: F 405 MET cc_start: 0.8590 (ppp) cc_final: 0.8192 (ppp) REVERT: G 163 ASN cc_start: 0.8974 (t0) cc_final: 0.8703 (t0) REVERT: H 140 MET cc_start: 0.8264 (ppp) cc_final: 0.6904 (ppp) REVERT: I 99 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8756 (pp30) REVERT: I 340 MET cc_start: 0.8851 (tmm) cc_final: 0.8366 (tmm) REVERT: I 564 MET cc_start: 0.8617 (mpp) cc_final: 0.8234 (mpp) REVERT: I 858 MET cc_start: 0.8671 (mtm) cc_final: 0.8424 (ttm) REVERT: I 880 MET cc_start: 0.8106 (mpp) cc_final: 0.7863 (mpp) REVERT: I 1005 MET cc_start: 0.8647 (mpp) cc_final: 0.8410 (mpp) REVERT: J 90 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8176 (tpp) REVERT: J 456 MET cc_start: 0.3101 (ttp) cc_final: 0.2312 (ttp) REVERT: J 481 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8761 (tpp) REVERT: J 661 MET cc_start: 0.9168 (ppp) cc_final: 0.8721 (ppp) REVERT: J 1045 MET cc_start: 0.8477 (mmm) cc_final: 0.8259 (mmm) REVERT: J 1219 GLU cc_start: 0.8876 (pp20) cc_final: 0.8469 (pp20) REVERT: K 88 GLU cc_start: 0.7412 (tp30) cc_final: 0.6225 (pt0) outliers start: 73 outliers final: 48 residues processed: 287 average time/residue: 0.2278 time to fit residues: 114.7358 Evaluate side-chains 269 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 215 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 404 GLU 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 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 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 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 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 F residue 334 MET Chi-restraints excluded: chain G residue 46 SER 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 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 269 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 637 LEU Chi-restraints excluded: chain I residue 865 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 237 optimal weight: 10.0000 chunk 479 optimal weight: 0.7980 chunk 453 optimal weight: 10.0000 chunk 465 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 411 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 302 optimal weight: 6.9990 chunk 325 optimal weight: 9.9990 chunk 513 optimal weight: 50.0000 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 138 ASN ** F 148 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.060314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.044246 restraints weight = 299148.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.045523 restraints weight = 175638.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046348 restraints weight = 124321.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.046892 restraints weight = 98759.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.047239 restraints weight = 84985.359| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 43482 Z= 0.148 Angle : 0.674 10.703 59185 Z= 0.333 Chirality : 0.044 0.263 6760 Planarity : 0.005 0.120 7415 Dihedral : 13.612 175.349 6806 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.10 % Favored : 93.82 % Rotamer: Outliers : 1.79 % Allowed : 15.40 % Favored : 82.81 % 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: -0.56 (0.12), residues: 5117 helix: 0.43 (0.12), residues: 1951 sheet: -0.66 (0.19), residues: 683 loop : -0.87 (0.13), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 259 TYR 0.037 0.001 TYR J 868 PHE 0.022 0.001 PHE D 419 TRP 0.043 0.002 TRP J 21 HIS 0.005 0.001 HIS J1103 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (43464) covalent geometry : angle 0.67038 / 0.33 (59173) hydrogen bonds : bond 0.04196 / 2.85 ( 1802) hydrogen bonds : angle 5.51450 / 3.90 ( 5048) metal coordination : bond 0.00768 / 0.42 ( 8) metal coordination : angle 4.93246 / 3.72 ( 12) Misc. bond : bond 0.00132 / 0.09 ( 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 301 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 223 time to evaluate : 1.909 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: A 105 TYR cc_start: 0.8313 (t80) cc_final: 0.8047 (t80) REVERT: A 405 MET cc_start: 0.8919 (ppp) cc_final: 0.8079 (ppp) REVERT: B 61 LEU cc_start: 0.9046 (tt) cc_final: 0.8699 (mm) REVERT: B 98 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: B 268 MET cc_start: 0.8810 (tpp) cc_final: 0.8486 (tpp) REVERT: B 348 MET cc_start: 0.8091 (mmm) cc_final: 0.7697 (tpp) REVERT: B 405 MET cc_start: 0.8893 (ppp) cc_final: 0.8581 (ppp) REVERT: C 348 MET cc_start: 0.8378 (mmm) cc_final: 0.7751 (mmm) REVERT: D 105 TYR cc_start: 0.9198 (t80) cc_final: 0.8732 (t80) REVERT: D 132 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8661 (t0) REVERT: D 387 MET cc_start: 0.7835 (ptt) cc_final: 0.7006 (ppp) REVERT: E 225 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8917 (t80) REVERT: E 348 MET cc_start: 0.7641 (mmm) cc_final: 0.7248 (mpp) REVERT: F 348 MET cc_start: 0.7840 (tpt) cc_final: 0.7403 (mmm) REVERT: F 405 MET cc_start: 0.8590 (ppp) cc_final: 0.8141 (ppp) REVERT: G 163 ASN cc_start: 0.8974 (t0) cc_final: 0.8699 (t0) REVERT: H 140 MET cc_start: 0.8374 (ppp) cc_final: 0.7161 (ppp) REVERT: I 99 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8758 (pp30) REVERT: I 340 MET cc_start: 0.8857 (tmm) cc_final: 0.8378 (tmm) REVERT: I 564 MET cc_start: 0.8740 (mpp) cc_final: 0.8336 (mpp) REVERT: I 858 MET cc_start: 0.8648 (ttm) cc_final: 0.8422 (ttm) REVERT: I 880 MET cc_start: 0.8140 (mpp) cc_final: 0.7887 (mpp) REVERT: I 1005 MET cc_start: 0.8639 (mpp) cc_final: 0.8384 (mpp) REVERT: I 1031 ARG cc_start: 0.8117 (mpt180) cc_final: 0.7727 (mmt180) REVERT: J 90 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8153 (tpp) REVERT: J 456 MET cc_start: 0.3193 (ttp) cc_final: 0.2426 (ttp) REVERT: J 481 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8806 (tpp) REVERT: J 661 MET cc_start: 0.9155 (ppp) cc_final: 0.8727 (ppp) REVERT: J 1219 GLU cc_start: 0.8877 (pp20) cc_final: 0.8464 (pp20) REVERT: K 88 GLU cc_start: 0.7434 (tp30) cc_final: 0.6221 (pt0) outliers start: 78 outliers final: 53 residues processed: 283 average time/residue: 0.2329 time to fit residues: 115.7790 Evaluate side-chains 269 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 210 time to evaluate : 1.830 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 1001 VAL 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 J residue 829 VAL Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 47 LYS 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: 5.9990 chunk 515 optimal weight: 40.0000 chunk 426 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 462 optimal weight: 1.9990 chunk 195 optimal weight: 0.3980 chunk 139 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 385 optimal weight: 7.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.060398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.044282 restraints weight = 298577.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.045526 restraints weight = 174818.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.046398 restraints weight = 124273.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.046954 restraints weight = 98196.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.047317 restraints weight = 84194.786| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2608 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= 0.141 Angle : 0.668 11.094 59185 Z= 0.330 Chirality : 0.043 0.236 6760 Planarity : 0.005 0.119 7415 Dihedral : 13.510 173.674 6806 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.94 % Favored : 93.98 % Rotamer: Outliers : 1.77 % Allowed : 16.02 % Favored : 82.22 % 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: -0.50 (0.12), residues: 5117 helix: 0.48 (0.12), residues: 1952 sheet: -0.64 (0.20), residues: 671 loop : -0.84 (0.13), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 166 TYR 0.028 0.001 TYR J 868 PHE 0.022 0.001 PHE D 419 TRP 0.077 0.002 TRP J 21 HIS 0.006 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (43464) covalent geometry : angle 0.66493 / 0.33 (59173) hydrogen bonds : bond 0.04060 / 2.76 ( 1802) hydrogen bonds : angle 5.42973 / 3.84 ( 5048) metal coordination : bond 0.00704 / 0.39 ( 8) metal coordination : angle 4.76262 / 3.61 ( 12) Misc. bond : bond 0.00135 / 0.09 ( 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 295 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 218 time to evaluate : 1.713 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: 0.8342 (t80) cc_final: 0.8051 (t80) REVERT: A 397 MET cc_start: 0.6745 (tmm) cc_final: 0.6341 (tmm) REVERT: A 405 MET cc_start: 0.8504 (ppp) cc_final: 0.8146 (ppp) REVERT: B 61 LEU cc_start: 0.9039 (tt) cc_final: 0.8690 (mm) REVERT: B 98 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: B 268 MET cc_start: 0.8822 (tpp) cc_final: 0.8497 (tpp) REVERT: B 348 MET cc_start: 0.8077 (mmm) cc_final: 0.7717 (tpp) REVERT: B 405 MET cc_start: 0.8909 (ppp) cc_final: 0.8653 (ppp) REVERT: C 225 PHE cc_start: 0.9243 (t80) cc_final: 0.8565 (t80) REVERT: C 348 MET cc_start: 0.8380 (mmm) cc_final: 0.7613 (mmm) REVERT: C 403 MET cc_start: 0.8932 (mmt) cc_final: 0.8698 (mmm) REVERT: D 105 TYR cc_start: 0.9170 (t80) cc_final: 0.8717 (t80) REVERT: D 132 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8666 (t0) REVERT: D 387 MET cc_start: 0.7714 (ptt) cc_final: 0.6932 (ppp) REVERT: E 225 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8905 (t80) REVERT: E 348 MET cc_start: 0.7632 (mmm) cc_final: 0.7212 (mpp) REVERT: E 405 MET cc_start: 0.9604 (tmm) cc_final: 0.8945 (ppp) REVERT: F 348 MET cc_start: 0.7884 (tpt) cc_final: 0.7393 (mmm) REVERT: F 403 MET cc_start: 0.9308 (tmm) cc_final: 0.9087 (ppp) REVERT: F 405 MET cc_start: 0.8651 (ppp) cc_final: 0.8189 (ppp) REVERT: G 123 MET cc_start: 0.8434 (mmm) cc_final: 0.7914 (mpp) REVERT: G 163 ASN cc_start: 0.8970 (t0) cc_final: 0.8697 (t0) REVERT: H 140 MET cc_start: 0.8386 (ppp) cc_final: 0.7194 (ppp) REVERT: I 99 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8758 (pp30) REVERT: I 340 MET cc_start: 0.8852 (tmm) cc_final: 0.8370 (tmm) REVERT: I 858 MET cc_start: 0.8618 (ttm) cc_final: 0.8386 (ttm) REVERT: I 880 MET cc_start: 0.8115 (mpp) cc_final: 0.7885 (mpp) REVERT: I 1005 MET cc_start: 0.8619 (mpp) cc_final: 0.8335 (mpp) REVERT: I 1031 ARG cc_start: 0.8078 (mpt180) cc_final: 0.7662 (mpt180) REVERT: J 90 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8114 (tpp) REVERT: J 456 MET cc_start: 0.3138 (ttp) cc_final: 0.2515 (ttp) REVERT: J 481 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8809 (tpp) REVERT: J 661 MET cc_start: 0.9180 (ppp) cc_final: 0.8738 (ppp) REVERT: J 745 MET cc_start: 0.8561 (ttt) cc_final: 0.8232 (ttm) REVERT: J 902 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8529 (pp) REVERT: J 1219 GLU cc_start: 0.8877 (pp20) cc_final: 0.8485 (pp20) REVERT: K 12 MET cc_start: 0.8881 (ppp) cc_final: 0.8592 (ppp) REVERT: K 88 GLU cc_start: 0.7442 (tp30) cc_final: 0.6222 (pt0) outliers start: 77 outliers final: 56 residues processed: 278 average time/residue: 0.2323 time to fit residues: 113.7872 Evaluate side-chains 273 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 210 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 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 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 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 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 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 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 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 566 THR Chi-restraints excluded: chain I residue 581 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 1097 LEU 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 29 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 476 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 516 optimal weight: 30.0000 chunk 5 optimal weight: 30.0000 chunk 269 optimal weight: 5.9990 chunk 305 optimal weight: 1.9990 chunk 266 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** F 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** ** 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 = 0.3672 r_free = 0.3672 target = 0.059777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.043716 restraints weight = 302450.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.044960 restraints weight = 177701.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.045774 restraints weight = 125943.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.046302 restraints weight = 100618.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.046641 restraints weight = 86778.460| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 43482 Z= 0.170 Angle : 0.686 11.460 59185 Z= 0.338 Chirality : 0.044 0.292 6760 Planarity : 0.005 0.118 7415 Dihedral : 13.457 170.664 6806 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.88 % Rotamer: Outliers : 1.79 % Allowed : 16.36 % Favored : 81.85 % 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: -0.50 (0.12), residues: 5117 helix: 0.50 (0.12), residues: 1955 sheet: -0.64 (0.20), residues: 673 loop : -0.85 (0.13), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 166 TYR 0.024 0.001 TYR J1207 PHE 0.022 0.002 PHE D 419 TRP 0.082 0.002 TRP J 21 HIS 0.004 0.001 HIS E 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (43464) covalent geometry : angle 0.68303 / 0.34 (59173) hydrogen bonds : bond 0.04157 / 2.84 ( 1802) hydrogen bonds : angle 5.41284 / 3.82 ( 5048) metal coordination : bond 0.00921 / 0.51 ( 8) metal coordination : angle 4.74990 / 3.66 ( 12) Misc. bond : bond 0.00133 / 0.09 ( 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 293 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 215 time to evaluate : 1.564 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: A 256 ARG cc_start: 0.8945 (mtp-110) cc_final: 0.8728 (mtm110) REVERT: A 397 MET cc_start: 0.7028 (tmm) cc_final: 0.6734 (tmm) REVERT: A 405 MET cc_start: 0.8473 (ppp) cc_final: 0.8155 (ppp) REVERT: B 98 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7590 (m-80) REVERT: B 268 MET cc_start: 0.8872 (tpp) cc_final: 0.8406 (tpp) REVERT: B 270 LEU cc_start: 0.8919 (mp) cc_final: 0.8325 (mt) REVERT: B 348 MET cc_start: 0.8106 (mmm) cc_final: 0.6853 (mmm) REVERT: B 405 MET cc_start: 0.8912 (ppp) cc_final: 0.8673 (ppp) REVERT: C 84 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: C 348 MET cc_start: 0.8393 (mmm) cc_final: 0.7619 (mmm) REVERT: C 403 MET cc_start: 0.8965 (mmt) cc_final: 0.8737 (mmm) REVERT: D 105 TYR cc_start: 0.9182 (t80) cc_final: 0.8741 (t80) REVERT: D 132 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8668 (t0) REVERT: D 387 MET cc_start: 0.7842 (ptt) cc_final: 0.7026 (ppp) REVERT: E 225 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8946 (t80) REVERT: E 405 MET cc_start: 0.9611 (tmm) cc_final: 0.8921 (ppp) REVERT: F 348 MET cc_start: 0.7911 (tpt) cc_final: 0.7359 (mmm) REVERT: F 403 MET cc_start: 0.9337 (tmm) cc_final: 0.9105 (ppp) REVERT: G 163 ASN cc_start: 0.9011 (t0) cc_final: 0.8638 (t0) REVERT: H 140 MET cc_start: 0.8440 (ppp) cc_final: 0.7242 (ppp) REVERT: I 99 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8765 (pp30) REVERT: I 340 MET cc_start: 0.8878 (tmm) cc_final: 0.8400 (tmm) REVERT: I 564 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8391 (mpp) REVERT: I 858 MET cc_start: 0.8667 (ttm) cc_final: 0.8390 (ttm) REVERT: I 880 MET cc_start: 0.8136 (mpp) cc_final: 0.7893 (mpp) REVERT: I 1005 MET cc_start: 0.8622 (mpp) cc_final: 0.8340 (mpp) REVERT: I 1031 ARG cc_start: 0.8120 (mpt180) cc_final: 0.7025 (mmt180) REVERT: J 90 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8154 (tpp) REVERT: J 456 MET cc_start: 0.2952 (ttp) cc_final: 0.2299 (ttp) REVERT: J 481 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8771 (tpp) REVERT: J 661 MET cc_start: 0.9169 (ppp) cc_final: 0.8731 (ppp) REVERT: J 902 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8562 (pp) REVERT: J 1219 GLU cc_start: 0.8870 (pp20) cc_final: 0.8470 (pp20) REVERT: K 12 MET cc_start: 0.8950 (ppp) cc_final: 0.8654 (ppp) REVERT: K 52 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7523 (mm-30) REVERT: K 88 GLU cc_start: 0.7590 (tp30) cc_final: 0.6331 (pt0) outliers start: 78 outliers final: 57 residues processed: 279 average time/residue: 0.2192 time to fit residues: 106.6306 Evaluate side-chains 279 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 213 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 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 84 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 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 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 F residue 123 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 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 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 290 LEU Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 560 MET Chi-restraints excluded: chain I residue 564 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 905 ILE Chi-restraints excluded: chain I residue 1001 VAL Chi-restraints excluded: chain I residue 1097 LEU 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 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 K residue 29 GLN Chi-restraints excluded: chain K residue 47 LYS 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: 9.9990 chunk 192 optimal weight: 0.9980 chunk 507 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 350 optimal weight: 5.9990 chunk 497 optimal weight: 1.9990 chunk 474 optimal weight: 4.9990 chunk 513 optimal weight: 50.0000 chunk 11 optimal weight: 10.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN ** 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** ** I1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.060782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.044754 restraints weight = 299201.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.046066 restraints weight = 175347.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.046900 restraints weight = 123116.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.047488 restraints weight = 97569.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.047847 restraints weight = 83156.787| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 43482 Z= 0.124 Angle : 0.683 13.070 59185 Z= 0.333 Chirality : 0.044 0.508 6760 Planarity : 0.005 0.118 7415 Dihedral : 13.361 170.899 6806 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.73 % Favored : 94.20 % Rotamer: Outliers : 1.54 % Allowed : 16.70 % Favored : 81.76 % 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: 1953 sheet: -0.63 (0.20), residues: 674 loop : -0.81 (0.13), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 373 TYR 0.025 0.001 TYR J 868 PHE 0.022 0.001 PHE D 419 TRP 0.061 0.002 TRP J 21 HIS 0.006 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (43464) covalent geometry : angle 0.67961 / 0.33 (59173) hydrogen bonds : bond 0.03865 / 2.60 ( 1802) hydrogen bonds : angle 5.27559 / 3.73 ( 5048) metal coordination : bond 0.00540 / 0.28 ( 8) metal coordination : angle 4.52669 / 3.45 ( 12) Misc. bond : bond 0.00126 / 0.09 ( 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 293 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 226 time to evaluate : 1.333 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: 0.8460 (t80) cc_final: 0.8131 (t80) REVERT: A 397 MET cc_start: 0.6814 (tmm) cc_final: 0.6439 (tmm) REVERT: A 405 MET cc_start: 0.8464 (ppp) cc_final: 0.8120 (ppp) REVERT: B 98 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7581 (m-80) REVERT: B 268 MET cc_start: 0.8835 (tpp) cc_final: 0.8343 (tpp) REVERT: B 270 LEU cc_start: 0.8882 (mp) cc_final: 0.8268 (mt) REVERT: B 340 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9192 (pp20) REVERT: B 348 MET cc_start: 0.7990 (mmm) cc_final: 0.7676 (tpp) REVERT: B 405 MET cc_start: 0.8925 (ppp) cc_final: 0.8693 (ppp) REVERT: C 84 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: C 225 PHE cc_start: 0.9212 (t80) cc_final: 0.8534 (t80) REVERT: C 341 GLU cc_start: 0.9572 (OUTLIER) cc_final: 0.9253 (pp20) REVERT: C 348 MET cc_start: 0.8276 (mmm) cc_final: 0.7613 (mmm) REVERT: C 403 MET cc_start: 0.8988 (mmt) cc_final: 0.8733 (mmm) REVERT: D 79 ASN cc_start: 0.8924 (t0) cc_final: 0.8591 (p0) REVERT: D 105 TYR cc_start: 0.9144 (t80) cc_final: 0.8693 (t80) REVERT: D 132 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8634 (t0) REVERT: D 313 ASN cc_start: 0.7145 (OUTLIER) cc_final: 0.6714 (t0) REVERT: D 387 MET cc_start: 0.7697 (ptt) cc_final: 0.6882 (ppp) REVERT: E 225 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8921 (t80) REVERT: E 348 MET cc_start: 0.7982 (mmm) cc_final: 0.7386 (mmp) REVERT: E 405 MET cc_start: 0.9599 (tmm) cc_final: 0.8901 (ppp) REVERT: F 348 MET cc_start: 0.7839 (tpt) cc_final: 0.7396 (mmm) REVERT: G 123 MET cc_start: 0.8450 (mmm) cc_final: 0.7938 (mpp) REVERT: G 163 ASN cc_start: 0.9023 (t0) cc_final: 0.8670 (t0) REVERT: H 140 MET cc_start: 0.8400 (ppp) cc_final: 0.7194 (ppp) REVERT: I 91 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8576 (pm20) REVERT: I 99 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8699 (pp30) REVERT: I 340 MET cc_start: 0.8859 (tmm) cc_final: 0.8358 (tmm) REVERT: I 880 MET cc_start: 0.8106 (mpp) cc_final: 0.7892 (mpp) REVERT: I 1005 MET cc_start: 0.8585 (mpp) cc_final: 0.8313 (mpp) REVERT: J 90 MET cc_start: 0.8328 (ttt) cc_final: 0.8071 (tpp) REVERT: J 456 MET cc_start: 0.2739 (ttp) cc_final: 0.2125 (ttp) REVERT: J 481 MET cc_start: 0.9069 (tpp) cc_final: 0.8786 (tpp) REVERT: J 661 MET cc_start: 0.9171 (ppp) cc_final: 0.8720 (ppp) REVERT: J 745 MET cc_start: 0.8572 (ttt) cc_final: 0.8223 (ttm) REVERT: J 902 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8508 (pp) REVERT: J 1219 GLU cc_start: 0.8825 (pp20) cc_final: 0.8427 (pp20) REVERT: K 12 MET cc_start: 0.8970 (ppp) cc_final: 0.8625 (ppp) REVERT: K 88 GLU cc_start: 0.7492 (tp30) cc_final: 0.6194 (pt0) REVERT: K 89 MET cc_start: 0.6859 (tpt) cc_final: 0.6512 (tpt) outliers start: 67 outliers final: 49 residues processed: 282 average time/residue: 0.2162 time to fit residues: 106.2889 Evaluate side-chains 274 residues out of total 4352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 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 C residue 84 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 341 GLU 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 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 F residue 123 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 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 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 1001 VAL Chi-restraints excluded: chain I residue 1106 ASP Chi-restraints excluded: chain J residue 127 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 1381 VAL Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 47 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 40 optimal weight: 30.0000 chunk 146 optimal weight: 3.9990 chunk 367 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 422 optimal weight: 2.9990 chunk 357 optimal weight: 3.9990 chunk 344 optimal weight: 9.9990 chunk 273 optimal weight: 4.9990 chunk 381 optimal weight: 8.9990 chunk 373 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 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** ** I1093 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 = 0.3670 r_free = 0.3670 target = 0.059671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.043580 restraints weight = 305534.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.044854 restraints weight = 180146.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.045684 restraints weight = 127004.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.046214 restraints weight = 101159.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.046559 restraints weight = 87142.152| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2987 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= 0.175 Angle : 0.706 19.005 59185 Z= 0.345 Chirality : 0.044 0.322 6760 Planarity : 0.005 0.117 7415 Dihedral : 13.352 166.019 6806 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.88 % Favored : 94.04 % Rotamer: Outliers : 1.52 % Allowed : 16.82 % Favored : 81.66 % 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: -0.44 (0.12), residues: 5117 helix: 0.52 (0.12), residues: 1958 sheet: -0.62 (0.20), residues: 659 loop : -0.79 (0.13), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 867 TYR 0.057 0.001 TYR J 868 PHE 0.021 0.002 PHE I1032 TRP 0.068 0.002 TRP J 21 HIS 0.008 0.001 HIS I 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (43464) covalent geometry : angle 0.70282 / 0.35 (59173) hydrogen bonds : bond 0.04045 / 2.76 ( 1802) hydrogen bonds : angle 5.31730 / 3.76 ( 5048) metal coordination : bond 0.00935 / 0.52 ( 8) metal coordination : angle 4.58634 / 3.54 ( 12) Misc. bond : bond 0.00121 / 0.08 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7666.02 seconds wall clock time: 133 minutes 12.04 seconds (7992.04 seconds total)