Starting phenix.real_space_refine on Wed May 28 09:17:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u72_41966/05_2025/8u72_41966.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u72_41966/05_2025/8u72_41966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u72_41966/05_2025/8u72_41966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u72_41966/05_2025/8u72_41966.map" model { file = "/net/cci-nas-00/data/ceres_data/8u72_41966/05_2025/8u72_41966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u72_41966/05_2025/8u72_41966.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.025 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1436 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 148 5.49 5 Mg 4 5.21 5 S 74 5.16 5 C 18877 2.51 5 N 5036 2.21 5 O 5573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29712 Number of models: 1 Model: "" Number of chains: 31 Chain: "U" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNA': 19} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "V" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "H" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3143 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 12, 'TRANS': 404} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 359 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 20, 'TYR:plan': 5, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 234 Chain: "I" Number of atoms: 3533 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3529 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 25, 'TRANS': 428} Chain breaks: 1 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 90 Conformer: "B" Number of residues, atoms: 454, 3529 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 25, 'TRANS': 428} Chain breaks: 1 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 90 bond proxies already assigned to first conformer: 3615 Chain: "E" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3452 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 25, 'TRANS': 426} Chain breaks: 1 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 137 Chain: "M" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNA': 19} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "N" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "S" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNA': 19} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "T" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "X" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNA': 19} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "Y" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3142 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 14, 'TRANS': 396} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 14, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 203 Chain: "B" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3166 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 14, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 276 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 19, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 234 Chain: "C" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3489 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 25, 'TRANS': 426} Chain breaks: 2 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 108 Chain: "F" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3170 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 13, 'TRANS': 402} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 7, 'ASP:plan': 17, 'GLU:plan': 16, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 211 Chain: "G" Number of atoms: 3476 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 450, 3468 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 25, 'TRANS': 424} Chain breaks: 3 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 116 Conformer: "B" Number of residues, atoms: 450, 3468 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 25, 'TRANS': 424} Chain breaks: 3 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 116 bond proxies already assigned to first conformer: 3546 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 22.24, per 1000 atoms: 0.75 Number of scatterers: 29712 At special positions: 0 Unit cell: (126.711, 170.031, 222.015, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 74 16.00 P 148 15.00 Mg 4 11.99 O 5573 8.00 N 5036 7.00 C 18877 6.00 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.79 Conformation dependent library (CDL) restraints added in 4.0 seconds 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6594 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 39 sheets defined 34.9% alpha, 18.4% beta 36 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 9.77 Creating SS restraints... Processing helix chain 'H' and resid 15 through 29 Processing helix chain 'H' and resid 44 through 56 removed outlier: 4.068A pdb=" N THR H 48 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE H 49 " --> pdb=" O PHE H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 89 Processing helix chain 'H' and resid 123 through 138 Processing helix chain 'H' and resid 150 through 159 Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 233 through 237 Processing helix chain 'H' and resid 242 through 247 Processing helix chain 'H' and resid 257 through 277 removed outlier: 3.776A pdb=" N ILE H 265 " --> pdb=" O CYS H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 304 removed outlier: 3.919A pdb=" N ASP H 303 " --> pdb=" O LEU H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 365 removed outlier: 3.685A pdb=" N LYS H 363 " --> pdb=" O SER H 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 368 No H-bonds generated for 'chain 'H' and resid 366 through 368' Processing helix chain 'H' and resid 369 through 385 removed outlier: 3.842A pdb=" N LYS H 376 " --> pdb=" O LYS H 372 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU H 384 " --> pdb=" O PHE H 380 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER H 385 " --> pdb=" O ILE H 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 17 No H-bonds generated for 'chain 'I' and resid 15 through 17' Processing helix chain 'I' and resid 22 through 30 Processing helix chain 'I' and resid 46 through 60 Processing helix chain 'I' and resid 77 through 83 Processing helix chain 'I' and resid 97 through 106 removed outlier: 3.633A pdb=" N PHE I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 131 removed outlier: 3.541A pdb=" N THR I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 149 removed outlier: 3.843A pdb=" N TYR I 148 " --> pdb=" O PRO I 144 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 144 through 149' Processing helix chain 'I' and resid 204 through 218 Processing helix chain 'I' and resid 226 through 230 Processing helix chain 'I' and resid 248 through 264 removed outlier: 3.702A pdb=" N ALA I 253 " --> pdb=" O GLU I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 351 Processing helix chain 'I' and resid 366 through 377 Processing helix chain 'I' and resid 451 through 464 removed outlier: 3.577A pdb=" N VAL I 455 " --> pdb=" O GLU I 451 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU I 456 " --> pdb=" O ILE I 452 " (cutoff:3.500A) Processing helix chain 'I' and resid 477 through 491 removed outlier: 3.637A pdb=" N ARG I 481 " --> pdb=" O PRO I 477 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA I 483 " --> pdb=" O THR I 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 22 through 30 removed outlier: 3.996A pdb=" N ALA E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 60 Processing helix chain 'E' and resid 77 through 83 Processing helix chain 'E' and resid 97 through 106 Processing helix chain 'E' and resid 110 through 131 removed outlier: 3.532A pdb=" N TYR E 115 " --> pdb=" O HIS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 248 through 264 removed outlier: 3.928A pdb=" N ALA E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP E 254 " --> pdb=" O GLY E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 291 No H-bonds generated for 'chain 'E' and resid 289 through 291' Processing helix chain 'E' and resid 331 through 351 removed outlier: 3.662A pdb=" N GLN E 349 " --> pdb=" O SER E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 377 removed outlier: 3.529A pdb=" N ASN E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 464 Processing helix chain 'E' and resid 477 through 492 removed outlier: 3.703A pdb=" N ARG E 481 " --> pdb=" O PRO E 477 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 507 removed outlier: 4.057A pdb=" N TYR E 506 " --> pdb=" O ALA E 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 29 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 71 through 89 removed outlier: 3.561A pdb=" N HIS D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 139 removed outlier: 3.528A pdb=" N GLY D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 158 removed outlier: 3.752A pdb=" N TYR D 154 " --> pdb=" O SER D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 257 through 277 removed outlier: 3.951A pdb=" N GLN D 262 " --> pdb=" O ASN D 258 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN D 267 " --> pdb=" O ARG D 263 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.820A pdb=" N ASP D 303 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.995A pdb=" N SER D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 385 removed outlier: 3.586A pdb=" N LEU D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 28 Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 72 through 89 Processing helix chain 'B' and resid 123 through 139 Processing helix chain 'B' and resid 147 through 159 removed outlier: 4.009A pdb=" N ASN B 151 " --> pdb=" O HIS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.548A pdb=" N ARG B 263 " --> pdb=" O TYR B 259 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.526A pdb=" N LYS B 304 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.957A pdb=" N SER B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 371 through 384 removed outlier: 3.724A pdb=" N LYS B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 22 through 30 Processing helix chain 'C' and resid 46 through 61 removed outlier: 3.518A pdb=" N GLN C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 83 Processing helix chain 'C' and resid 97 through 105 removed outlier: 3.533A pdb=" N ILE C 101 " --> pdb=" O THR C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 131 Processing helix chain 'C' and resid 204 through 218 removed outlier: 4.063A pdb=" N GLU C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N HIS C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 248 through 264 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 366 through 377 Processing helix chain 'C' and resid 451 through 464 Processing helix chain 'C' and resid 477 through 491 removed outlier: 3.697A pdb=" N ARG C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 28 removed outlier: 3.772A pdb=" N ASP F 15 " --> pdb=" O THR F 11 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASP F 16 " --> pdb=" O PRO F 12 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR F 18 " --> pdb=" O ASP F 14 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU F 28 " --> pdb=" O LYS F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 56 Processing helix chain 'F' and resid 71 through 89 removed outlier: 3.640A pdb=" N HIS F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 138 Processing helix chain 'F' and resid 150 through 162 removed outlier: 3.534A pdb=" N ILE F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS F 162 " --> pdb=" O PHE F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 245 No H-bonds generated for 'chain 'F' and resid 243 through 245' Processing helix chain 'F' and resid 257 through 277 removed outlier: 4.275A pdb=" N MET F 277 " --> pdb=" O PHE F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 removed outlier: 3.945A pdb=" N LYS F 304 " --> pdb=" O GLU F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 365 removed outlier: 3.605A pdb=" N HIS F 358 " --> pdb=" O LYS F 354 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS F 363 " --> pdb=" O SER F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 384 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 30 Processing helix chain 'G' and resid 46 through 61 Processing helix chain 'G' and resid 77 through 83 Processing helix chain 'G' and resid 97 through 105 Processing helix chain 'G' and resid 112 through 131 removed outlier: 3.860A pdb=" N VAL G 118 " --> pdb=" O THR G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 216 Processing helix chain 'G' and resid 226 through 230 Processing helix chain 'G' and resid 248 through 264 Processing helix chain 'G' and resid 331 through 351 Processing helix chain 'G' and resid 366 through 377 Processing helix chain 'G' and resid 451 through 465 removed outlier: 3.631A pdb=" N VAL G 455 " --> pdb=" O GLU G 451 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU G 456 " --> pdb=" O ILE G 452 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU G 465 " --> pdb=" O ALA G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 493 removed outlier: 3.748A pdb=" N ARG G 481 " --> pdb=" O PRO G 477 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 483 " --> pdb=" O THR G 479 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER G 493 " --> pdb=" O ILE G 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 32 through 33 removed outlier: 3.519A pdb=" N TRP H 33 " --> pdb=" O ILE H 5 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS H 4 " --> pdb=" O CYS H 58 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE H 60 " --> pdb=" O LYS H 4 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE H 6 " --> pdb=" O PHE H 60 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE H 62 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER H 8 " --> pdb=" O ILE H 62 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N SER H 64 " --> pdb=" O SER H 8 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ILE H 118 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 295 through 299 removed outlier: 5.698A pdb=" N VAL I 278 " --> pdb=" O LEU I 305 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU I 305 " --> pdb=" O VAL I 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 295 through 299 removed outlier: 6.128A pdb=" N CYS I 279 " --> pdb=" O PHE I 358 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N HIS I 360 " --> pdb=" O CYS I 279 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU I 281 " --> pdb=" O HIS I 360 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS I 417 " --> pdb=" O VAL I 413 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE I 412 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU I 3 " --> pdb=" O ILE I 412 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS I 2 " --> pdb=" O LYS H 409 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 326 through 328 removed outlier: 7.153A pdb=" N LEU H 402 " --> pdb=" O ILE H 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 184 through 187 Processing sheet with id=AA6, first strand: chain 'H' and resid 283 through 286 Processing sheet with id=AA7, first strand: chain 'H' and resid 283 through 286 Processing sheet with id=AA8, first strand: chain 'I' and resid 19 through 20 Processing sheet with id=AA9, first strand: chain 'I' and resid 91 through 95 removed outlier: 6.308A pdb=" N GLY I 42 " --> pdb=" O PHE I 140 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE I 142 " --> pdb=" O GLY I 42 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL I 44 " --> pdb=" O ILE I 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 425 through 426 removed outlier: 3.844A pdb=" N SER I 431 " --> pdb=" O VAL I 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 311 through 320 removed outlier: 5.846A pdb=" N GLY E 318 " --> pdb=" O CYS E 298 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N CYS E 298 " --> pdb=" O GLY E 318 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TRP E 320 " --> pdb=" O ASN E 296 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN E 296 " --> pdb=" O TRP E 320 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA E 301 " --> pdb=" O GLY E 282 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR E 280 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N CYS E 279 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N HIS E 360 " --> pdb=" O CYS E 279 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU E 281 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR E 387 " --> pdb=" O ILE E 445 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE E 445 " --> pdb=" O THR E 387 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR E 389 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE E 443 " --> pdb=" O THR E 389 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS E 417 " --> pdb=" O VAL E 413 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE E 412 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLU E 3 " --> pdb=" O ILE E 412 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LYS E 2 " --> pdb=" O PHE D 411 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU D 169 " --> pdb=" O GLY D 412 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AB4, first strand: chain 'E' and resid 91 through 95 removed outlier: 3.627A pdb=" N GLY E 45 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLY E 42 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE E 142 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL E 44 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TRP E 139 " --> pdb=" O GLN E 222 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU E 224 " --> pdb=" O TRP E 139 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL E 141 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 425 through 426 removed outlier: 3.592A pdb=" N SER E 431 " --> pdb=" O VAL E 426 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 32 through 33 removed outlier: 6.173A pdb=" N ILE D 5 " --> pdb=" O TRP D 33 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LYS D 4 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU D 61 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE D 6 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL D 63 " --> pdb=" O PHE D 6 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER D 8 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE D 62 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 327 through 328 removed outlier: 3.529A pdb=" N LYS D 328 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU D 402 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 184 through 187 Processing sheet with id=AB9, first strand: chain 'D' and resid 283 through 286 Processing sheet with id=AC1, first strand: chain 'D' and resid 283 through 286 Processing sheet with id=AC2, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.418A pdb=" N ILE B 5 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS B 4 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LEU B 61 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE B 6 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL B 63 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N SER B 8 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 62 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 409 through 412 Processing sheet with id=AC4, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.508A pdb=" N PHE B 176 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 402 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 403 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 285 through 286 Processing sheet with id=AC6, first strand: chain 'C' and resid 5 through 6 removed outlier: 6.579A pdb=" N LYS C 417 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N CYS C 279 " --> pdb=" O PHE C 358 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N HIS C 360 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU C 281 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL C 278 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU C 305 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 5 through 6 removed outlier: 6.579A pdb=" N LYS C 417 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N CYS C 279 " --> pdb=" O PHE C 358 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N HIS C 360 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU C 281 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP C 320 " --> pdb=" O CYS C 298 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.508A pdb=" N LYS C 270 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 91 through 95 removed outlier: 6.293A pdb=" N GLY C 42 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE C 142 " --> pdb=" O GLY C 42 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C 44 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP C 139 " --> pdb=" O GLN C 222 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU C 224 " --> pdb=" O TRP C 139 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL C 141 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 235 through 236 removed outlier: 3.511A pdb=" N ASN C 236 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 425 through 426 removed outlier: 3.736A pdb=" N SER C 431 " --> pdb=" O VAL C 426 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 32 through 34 removed outlier: 3.583A pdb=" N ILE F 62 " --> pdb=" O ILE F 95 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 409 through 412 Processing sheet with id=AD5, first strand: chain 'F' and resid 293 through 294 removed outlier: 6.823A pdb=" N LEU F 402 " --> pdb=" O ILE F 179 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 217 through 218 removed outlier: 3.602A pdb=" N ALA F 218 " --> pdb=" O ARG F 186 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 5 through 6 removed outlier: 5.205A pdb=" N ILE G 443 " --> pdb=" O THR G 389 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR G 389 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE G 445 " --> pdb=" O THR G 387 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR G 387 " --> pdb=" O ILE G 445 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N CYS G 279 " --> pdb=" O PHE G 358 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N HIS G 360 " --> pdb=" O CYS G 279 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU G 281 " --> pdb=" O HIS G 360 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL G 278 " --> pdb=" O LEU G 305 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU G 305 " --> pdb=" O VAL G 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 5 through 6 removed outlier: 5.205A pdb=" N ILE G 443 " --> pdb=" O THR G 389 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR G 389 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE G 445 " --> pdb=" O THR G 387 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR G 387 " --> pdb=" O ILE G 445 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N CYS G 279 " --> pdb=" O PHE G 358 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N HIS G 360 " --> pdb=" O CYS G 279 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU G 281 " --> pdb=" O HIS G 360 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL G 278 " --> pdb=" O LEU G 305 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU G 305 " --> pdb=" O VAL G 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AE1, first strand: chain 'G' and resid 91 through 95 removed outlier: 3.520A pdb=" N VAL G 92 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY G 42 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE G 142 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL G 44 " --> pdb=" O ILE G 142 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 235 through 236 Processing sheet with id=AE3, first strand: chain 'G' and resid 425 through 426 removed outlier: 3.845A pdb=" N SER G 431 " --> pdb=" O VAL G 426 " (cutoff:3.500A) 1133 hydrogen bonds defined for protein. 3207 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 11.18 Time building geometry restraints manager: 7.92 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: 5024 1.33 - 1.45: 8660 1.45 - 1.57: 16611 1.57 - 1.69: 289 1.69 - 1.81: 103 Bond restraints: 30687 Sorted by residual: bond pdb=" N GLU E 476 " pdb=" CA GLU E 476 " ideal model delta sigma weight residual 1.456 1.500 -0.044 9.80e-03 1.04e+04 2.04e+01 bond pdb=" C ALA F 10 " pdb=" O ALA F 10 " ideal model delta sigma weight residual 1.232 1.289 -0.057 1.37e-02 5.33e+03 1.74e+01 bond pdb=" N SER F 8 " pdb=" CA SER F 8 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.87e+00 bond pdb=" N HIS F 9 " pdb=" CA HIS F 9 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.69e+00 bond pdb=" C GLU E 476 " pdb=" N PRO E 477 " ideal model delta sigma weight residual 1.332 1.364 -0.032 1.30e-02 5.92e+03 6.15e+00 ... (remaining 30682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 42119 3.19 - 6.38: 197 6.38 - 9.57: 23 9.57 - 12.76: 5 12.76 - 15.95: 1 Bond angle restraints: 42345 Sorted by residual: angle pdb=" O3' DA V 4 " pdb=" P DT V 5 " pdb=" O5' DT V 5 " ideal model delta sigma weight residual 104.00 119.95 -15.95 1.50e+00 4.44e-01 1.13e+02 angle pdb=" N ILE I 36 " pdb=" CA ILE I 36 " pdb=" C ILE I 36 " ideal model delta sigma weight residual 108.97 96.32 12.65 1.55e+00 4.16e-01 6.66e+01 angle pdb=" N ASP F 14 " pdb=" CA ASP F 14 " pdb=" C ASP F 14 " ideal model delta sigma weight residual 111.30 100.74 10.56 1.43e+00 4.89e-01 5.46e+01 angle pdb=" N LEU D 214 " pdb=" CA LEU D 214 " pdb=" C LEU D 214 " ideal model delta sigma weight residual 111.54 101.54 10.00 1.36e+00 5.41e-01 5.41e+01 angle pdb=" C TYR F 190 " pdb=" CA TYR F 190 " pdb=" CB TYR F 190 " ideal model delta sigma weight residual 111.73 120.17 -8.44 1.42e+00 4.96e-01 3.53e+01 ... (remaining 42340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.92: 16554 28.92 - 57.83: 1346 57.83 - 86.75: 161 86.75 - 115.66: 3 115.66 - 144.58: 4 Dihedral angle restraints: 18068 sinusoidal: 7912 harmonic: 10156 Sorted by residual: dihedral pdb=" CD ARG H 189 " pdb=" NE ARG H 189 " pdb=" CZ ARG H 189 " pdb=" NH1 ARG H 189 " ideal model delta sinusoidal sigma weight residual 0.00 -80.86 80.86 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CA MET F 277 " pdb=" C MET F 277 " pdb=" N LYS F 278 " pdb=" CA LYS F 278 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA GLY E 318 " pdb=" C GLY E 318 " pdb=" N PRO E 319 " pdb=" CA PRO E 319 " ideal model delta harmonic sigma weight residual -180.00 -153.33 -26.67 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 18065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 4857 0.161 - 0.322: 3 0.322 - 0.484: 1 0.484 - 0.645: 3 0.645 - 0.806: 1 Chirality restraints: 4865 Sorted by residual: chirality pdb=" P DT V 5 " pdb=" OP1 DT V 5 " pdb=" OP2 DT V 5 " pdb=" O5' DT V 5 " both_signs ideal model delta sigma weight residual True 2.35 -3.15 -0.81 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" P DT T 5 " pdb=" OP1 DT T 5 " pdb=" OP2 DT T 5 " pdb=" O5' DT T 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.62 2.00e-01 2.50e+01 9.47e+00 chirality pdb=" P DT N 5 " pdb=" OP1 DT N 5 " pdb=" OP2 DT N 5 " pdb=" O5' DT N 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.55e+00 ... (remaining 4862 not shown) Planarity restraints: 4793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 189 " 1.079 9.50e-02 1.11e+02 4.83e-01 1.41e+02 pdb=" NE ARG H 189 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG H 189 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG H 189 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG H 189 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS G 62 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO G 63 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO G 63 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 63 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 181 " -0.047 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO B 182 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 182 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 182 " -0.039 5.00e-02 4.00e+02 ... (remaining 4790 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 495 2.65 - 3.22: 25548 3.22 - 3.78: 43886 3.78 - 4.34: 62222 4.34 - 4.90: 101791 Nonbonded interactions: 233942 Sorted by model distance: nonbonded pdb=" OP1 U X 1 " pdb="MG MG G 601 " model vdw 2.092 2.170 nonbonded pdb=" OD1 ASP E 414 " pdb=" N GLU E 415 " model vdw 2.151 3.120 nonbonded pdb=" OP1 A M 3 " pdb="MG MG E 601 " model vdw 2.166 2.170 nonbonded pdb=" OP1 U U 1 " pdb="MG MG C 601 " model vdw 2.190 2.170 nonbonded pdb=" OG1 THR H 344 " pdb=" O ASN H 349 " model vdw 2.198 3.040 ... (remaining 233937 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 'B' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 7 or (resid 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 11 or (resid 12 through 16 and (name N or name CA \ or name C or name O or name CB )) or resid 17 through 23 or (resid 24 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name CE )) \ or resid 25 through 37 or (resid 38 and (name N or name CA or name C or name O \ or name CB )) or resid 46 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB or name CG or name CD )) or resid 60 through 65 or (resi \ d 66 through 67 and (name N or name CA or name C or name O or name CB )) or resi \ d 68 through 69 or (resid 70 and (name N or name CA or name C or name O or name \ CB )) or resid 71 through 76 or (resid 77 and (name N or name CA or name C or na \ me O or name CB )) or resid 78 through 91 or (resid 92 and (name N or name CA or \ name C or name O or name CB )) or resid 93 through 98 or (resid 99 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2)) or resid 100 \ through 103 or (resid 104 and (name N or name CA or name C or name O or name CB \ )) or resid 105 through 106 or (resid 107 and (name N or name CA or name C or n \ ame O or name CB )) or resid 108 through 113 or (resid 114 and (name N or name C \ A or name C or name O or name CB )) or resid 115 or (resid 116 through 117 and ( \ name N or name CA or name C or name O or name CB )) or resid 118 through 120 or \ (resid 121 through 122 and (name N or name CA or name C or name O or name CB )) \ or resid 123 through 129 or (resid 130 and (name N or name CA or name C or name \ O or name CB )) or resid 131 through 136 or (resid 137 and (name N or name CA or \ name C or name O or name CB )) or resid 138 or (resid 139 and (name N or name C \ A or name C or name O or name CB or name CG )) or resid 140 through 143 or (resi \ d 149 through 152 and (name N or name CA or name C or name O or name CB )) or re \ sid 153 or (resid 154 through 155 and (name N or name CA or name C or name O or \ name CB )) or resid 156 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 162 or (resid 163 through 164 an \ d (name N or name CA or name C or name O or name CB )) or resid 165 through 167 \ or (resid 168 through 169 and (name N or name CA or name C or name O or name CB \ )) or resid 170 through 183 or (resid 184 and (name N or name CA or name C or na \ me O or name CB )) or resid 185 through 188 or (resid 189 and (name N or name CA \ or name C or name O or name CB )) or (resid 190 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE \ 2 or name CZ )) or resid 191 through 198 or (resid 199 through 200 and (name N o \ r name CA or name C or name O or name CB )) or resid 201 through 226 or (resid 2 \ 27 through 234 and (name N or name CA or name C or name O or name CB )) or resid \ 235 through 256 or (resid 257 and (name N or name CA or name C or name O or nam \ e CB )) or resid 258 or (resid 259 and (name N or name CA or name C or name O or \ name CB )) or (resid 260 and (name N or name CA or name C or name O or name CB \ or name CG or name CD )) or resid 261 through 277 or (resid 278 through 279 and \ (name N or name CA or name C or name O or name CB )) or resid 280 through 283 or \ (resid 284 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 5 through 295 or (resid 296 through 297 and (name N or name CA or name C or name \ O or name CB )) or resid 298 or (resid 299 and (name N or name CA or name C or \ name O or name CB )) or resid 300 through 305 or (resid 306 through 307 and (nam \ e N or name CA or name C or name O or name CB )) or resid 308 through 327 or (re \ sid 328 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE )) or resid 329 through 347 or (resid 348 through 349 and (name N \ or name CA or name C or name O or name CB )) or resid 350 through 353 or (resid \ 354 and (name N or name CA or name C or name O or name CB )) or resid 355 throu \ gh 358 or (resid 359 and (name N or name CA or name C or name O or name CB )) or \ resid 360 through 362 or (resid 363 and (name N or name CA or name C or name O \ or name CB or name CG or name CD )) or resid 364 through 396 or (resid 397 throu \ gh 398 and (name N or name CA or name C or name O or name CB )) or resid 399 thr \ ough 420)) selection = (chain 'D' and (resid 3 through 11 or (resid 12 through 16 and (name N or name C \ A or name C or name O or name CB )) or resid 17 through 23 or (resid 24 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE ) \ ) or resid 25 through 47 or (resid 48 and (name N or name CA or name C or name O \ or name CB )) or resid 49 through 50 or (resid 51 through 52 and (name N or nam \ e CA or name C or name O or name CB )) or resid 53 or (resid 54 through 55 and ( \ name N or name CA or name C or name O or name CB )) or resid 56 through 58 or (r \ esid 59 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or resid 60 through 65 or (resid 66 through 67 and (name N or name CA or \ name C or name O or name CB )) or resid 68 through 70 or (resid 71 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD or name NE )) or \ resid 72 through 75 or (resid 76 through 77 and (name N or name CA or name C or \ name O or name CB )) or resid 78 through 82 or (resid 83 and (name N or name CA \ or name C or name O or name CB or name CG or name CD )) or resid 84 through 91 o \ r (resid 92 and (name N or name CA or name C or name O or name CB )) or resid 93 \ through 99 or (resid 100 through 102 and (name N or name CA or name C or name O \ or name CB )) or resid 103 or (resid 104 and (name N or name CA or name C or na \ me O or name CB )) or resid 105 through 106 or (resid 107 and (name N or name CA \ or name C or name O or name CB )) or resid 108 through 109 or (resid 110 and (n \ ame N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (re \ sid 111 and (name N or name CA or name C or name O or name CB )) or resid 112 th \ rough 113 or (resid 114 and (name N or name CA or name C or name O or name CB )) \ or resid 115 or (resid 116 through 117 and (name N or name CA or name C or name \ O or name CB )) or resid 118 through 120 or (resid 121 through 122 and (name N \ or name CA or name C or name O or name CB )) or resid 123 through 129 or (resid \ 130 and (name N or name CA or name C or name O or name CB )) or resid 131 throug \ h 136 or (resid 137 and (name N or name CA or name C or name O or name CB )) or \ (resid 138 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD )) or (resid 139 and (name N or name CA or name C or name O or name CB or \ name CG )) or resid 140 through 143 or (resid 149 through 152 and (name N or na \ me CA or name C or name O or name CB )) or resid 153 or (resid 154 through 155 a \ nd (name N or name CA or name C or name O or name CB )) or resid 156 through 157 \ or (resid 158 and (name N or name CA or name C or name O or name CB )) or resid \ 159 through 161 or (resid 162 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name CE )) or (resid 163 through 164 and (name N o \ r name CA or name C or name O or name CB )) or resid 165 through 167 or (resid 1 \ 68 through 169 and (name N or name CA or name C or name O or name CB )) or resid \ 170 through 188 or (resid 189 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 190 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 19 \ 1 through 192 or (resid 193 and (name N or name CA or name C or name O or name C \ B )) or resid 194 through 198 or (resid 199 through 200 and (name N or name CA o \ r name C or name O or name CB )) or resid 201 through 210 or (resid 211 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE ) \ ) or resid 212 through 226 or (resid 227 through 234 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 235 through 237 and (name N or name CA o \ r name C or name O or name CB )) or resid 238 through 242 or (resid 243 through \ 244 and (name N or name CA or name C or name O or name CB )) or resid 245 throug \ h 256 or (resid 257 and (name N or name CA or name C or name O or name CB )) or \ resid 258 or (resid 259 and (name N or name CA or name C or name O or name CB )) \ or (resid 260 and (name N or name CA or name C or name O or name CB or name CG \ or name CD )) or resid 261 through 283 or (resid 284 and (name N or name CA or n \ ame C or name O or name CB )) or resid 285 through 312 or (resid 313 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE )) o \ r resid 314 through 345 or (resid 346 and (name N or name CA or name C or name O \ or name CB )) or (resid 347 through 349 and (name N or name CA or name C or nam \ e O or name CB )) or resid 350 through 353 or (resid 354 and (name N or name CA \ or name C or name O or name CB )) or resid 355 through 370 or (resid 371 and (na \ me N or name CA or name C or name O or name CB )) or resid 372 through 390 or (r \ esid 391 and (name N or name CA or name C or name O or name CB or name CG1 or na \ me CG2)) or resid 392 through 412 or (resid 413 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or resid 414 through 420)) selection = (chain 'F' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 7 or (resid 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 18 or (resid 19 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name NE )) or resid 2 \ 0 through 23 or (resid 24 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE )) or resid 25 through 30 or (resid 31 and (nam \ e N or name CA or name C or name O or name CB )) or resid 32 through 34 or (resi \ d 35 and (name N or name CA or name C or name O or name CB )) or resid 36 throug \ h 37 or (resid 38 and (name N or name CA or name C or name O or name CB )) or re \ sid 46 through 47 or (resid 48 and (name N or name CA or name C or name O or nam \ e CB )) or resid 49 or (resid 50 through 52 and (name N or name CA or name C or \ name O or name CB )) or resid 53 or (resid 54 through 55 and (name N or name CA \ or name C or name O or name CB )) or resid 56 through 58 or (resid 59 and (name \ N or name CA or name C or name O or name CB or name CG or name CD )) or resid 60 \ through 65 or (resid 66 through 67 and (name N or name CA or name C or name O o \ r name CB )) or resid 68 through 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or (resid 71 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE )) or resid 72 through 75 or (resi \ d 76 through 77 and (name N or name CA or name C or name O or name CB )) or resi \ d 78 through 82 or (resid 83 and (name N or name CA or name C or name O or name \ CB or name CG or name CD )) or resid 84 through 98 or (resid 99 and (name N or n \ ame CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 100 th \ rough 102 and (name N or name CA or name C or name O or name CB )) or resid 103 \ through 106 or (resid 107 and (name N or name CA or name C or name O or name CB \ )) or resid 108 through 110 or (resid 111 and (name N or name CA or name C or na \ me O or name CB )) or (resid 112 through 113 and (name N or name CA or name C or \ name O or name CB or name CG1 or name CG2)) or (resid 114 and (name N or name C \ A or name C or name O or name CB )) or resid 115 through 120 or (resid 121 throu \ gh 122 and (name N or name CA or name C or name O or name CB )) or resid 123 thr \ ough 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) \ or resid 127 through 129 or (resid 130 and (name N or name CA or name C or name \ O or name CB )) or resid 131 through 137 or (resid 138 and (name N or name CA or \ name C or name O or name CB or name CG or name CD )) or resid 139 through 143 o \ r (resid 149 through 152 and (name N or name CA or name C or name O or name CB ) \ ) or resid 153 or (resid 154 through 155 and (name N or name CA or name C or nam \ e O or name CB )) or resid 156 through 157 or (resid 158 and (name N or name CA \ or name C or name O or name CB )) or resid 159 or (resid 160 through 161 and (na \ me N or name CA or name C or name O or name CB )) or resid 162 through 165 or (r \ esid 166 and (name N or name CA or name C or name O or name CB )) or resid 167 o \ r (resid 168 through 169 and (name N or name CA or name C or name O or name CB ) \ ) or resid 170 through 183 or (resid 184 and (name N or name CA or name C or nam \ e O or name CB )) or resid 185 through 225 or (resid 226 through 234 and (name N \ or name CA or name C or name O or name CB )) or resid 235 through 242 or (resid \ 243 through 244 and (name N or name CA or name C or name O or name CB )) or res \ id 245 through 295 or (resid 296 through 297 and (name N or name CA or name C or \ name O or name CB )) or resid 298 or (resid 299 and (name N or name CA or name \ C or name O or name CB )) or resid 300 through 305 or (resid 306 through 307 and \ (name N or name CA or name C or name O or name CB )) or resid 308 through 312 o \ r (resid 313 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name CE )) or resid 314 through 347 or (resid 348 through 349 and (n \ ame N or name CA or name C or name O or name CB )) or resid 350 through 353 or ( \ resid 354 and (name N or name CA or name C or name O or name CB )) or resid 355 \ through 358 or (resid 359 and (name N or name CA or name C or name O or name CB \ )) or resid 360 through 370 or (resid 371 and (name N or name CA or name C or na \ me O or name CB )) or resid 372 through 390 or (resid 391 and (name N or name CA \ or name C or name O or name CB or name CG1 or name CG2)) or resid 392 through 3 \ 96 or (resid 397 through 398 and (name N or name CA or name C or name O or name \ CB )) or resid 399 through 412 or (resid 413 and (name N or name CA or name C or \ name O or name CB or name CG or name CD )) or resid 414 through 420)) selection = (chain 'H' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 7 or (resid 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 11 or (resid 12 through 16 and (name N or name CA \ or name C or name O or name CB )) or resid 17 through 18 or (resid 19 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name NE )) \ or resid 20 through 30 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 46 through 47 or (resid 48 and (name N or na \ me CA or name C or name O or name CB )) or resid 49 or (resid 50 through 52 and \ (name N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 th \ rough 55 and (name N or name CA or name C or name O or name CB )) or resid 56 th \ rough 69 or (resid 70 and (name N or name CA or name C or name O or name CB )) o \ r (resid 71 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE )) or resid 72 through 75 or (resid 76 through 77 and (name N \ or name CA or name C or name O or name CB )) or resid 78 through 82 or (resid 8 \ 3 and (name N or name CA or name C or name O or name CB or name CG or name CD )) \ or resid 84 through 98 or (resid 99 and (name N or name CA or name C or name O \ or name CB or name CG1 or name CG2)) or (resid 100 through 102 and (name N or na \ me CA or name C or name O or name CB )) or resid 103 through 109 or (resid 110 a \ nd (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) o \ r resid 111 or (resid 112 through 113 and (name N or name CA or name C or name O \ or name CB or name CG1 or name CG2)) or resid 114 through 137 or (resid 138 and \ (name N or name CA or name C or name O or name CB or name CG or name CD )) or ( \ resid 139 and (name N or name CA or name C or name O or name CB or name CG )) or \ resid 140 through 143 or (resid 149 through 152 and (name N or name CA or name \ C or name O or name CB )) or resid 153 through 159 or (resid 160 through 161 and \ (name N or name CA or name C or name O or name CB )) or (resid 162 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE )) or \ resid 163 through 188 or (resid 189 and (name N or name CA or name C or name O \ or name CB )) or (resid 190 and (name N or name CA or name C or name O or name C \ B or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or re \ sid 191 through 192 or (resid 193 and (name N or name CA or name C or name O or \ name CB )) or resid 194 through 198 or (resid 199 through 200 and (name N or nam \ e CA or name C or name O or name CB )) or resid 201 through 210 or (resid 211 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e CE )) or resid 212 through 225 or (resid 226 through 234 and (name N or name C \ A or name C or name O or name CB )) or (resid 235 through 237 and (name N or nam \ e CA or name C or name O or name CB )) or resid 238 through 242 or (resid 243 th \ rough 244 and (name N or name CA or name C or name O or name CB )) or resid 245 \ through 256 or (resid 257 and (name N or name CA or name C or name O or name CB \ )) or resid 258 or (resid 259 and (name N or name CA or name C or name O or name \ CB )) or (resid 260 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD )) or resid 261 through 283 or (resid 284 and (name N or name C \ A or name C or name O or name CB )) or resid 285 through 295 or (resid 296 throu \ gh 297 and (name N or name CA or name C or name O or name CB )) or resid 298 thr \ ough 312 or (resid 313 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name CE )) or resid 314 through 327 or (resid 328 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE ) \ ) or resid 329 through 358 or (resid 359 and (name N or name CA or name C or nam \ e O or name CB )) or resid 360 through 362 or (resid 363 and (name N or name CA \ or name C or name O or name CB or name CG or name CD )) or resid 364 through 370 \ or (resid 371 and (name N or name CA or name C or name O or name CB )) or resid \ 372 through 390 or (resid 391 and (name N or name CA or name C or name O or nam \ e CB or name CG1 or name CG2)) or resid 392 through 396 or (resid 397 through 39 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 399 through \ 412 or (resid 413 and (name N or name CA or name C or name O or name CB or name \ CG or name CD )) or resid 414 through 420)) } ncs_group { reference = (chain 'C' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB or name CG )) or resid 4 through 7 or (resid 8 and (name N o \ r name CA or name C or name O or name CB )) or resid 9 through 34 or (resid 35 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD )) or \ resid 36 through 40 or (resid 41 and (name N or name CA or name C or name O or \ name CB )) or resid 42 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 50 or (resid 51 and (name N or name \ CA or name C or name O or name CB )) or (resid 52 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2)) or resid 53 through 57 or (res \ id 58 and (name N or name CA or name C or name O or name CB )) or (resid 59 and \ (name N or name CA or name C or name O or name CB or name CG or name CD )) or re \ sid 60 through 61 or (resid 62 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name CE )) or resid 63 through 67 or (resid 68 and \ (name N or name CA or name C or name O or name CB or name CG )) or resid 69 thr \ ough 71 or (resid 72 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name NE or name CZ )) or resid 73 through 84 or (resid 85 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e CE )) or resid 86 through 100 or (resid 101 through 102 and (name N or name CA \ or name C or name O or name CB )) or resid 103 or (resid 104 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name C \ E1 or name CE2 or name CZ )) or resid 105 through 106 or (resid 109 through 112 \ and (name N or name CA or name C or name O or name CB )) or resid 113 through 12 \ 2 or (resid 123 and (name N or name CA or name C or name O or name CB )) or resi \ d 124 through 133 or (resid 134 and (name N or name CA or name C or name O or na \ me CB )) or resid 135 through 147 or (resid 148 through 149 and (name N or name \ CA or name C or name O or name CB )) or resid 205 through 207 or (resid 208 and \ (name N or name CA or name C or name O or name CB )) or resid 209 through 215 or \ (resid 216 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 7 through 242 or resid 244 through 247 or (resid 248 and (name N or name CA or n \ ame C or name O or name CB or name CG1 or name CG2)) or resid 249 through 262 or \ (resid 263 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name CE )) or resid 264 through 266 or resid 268 through 302 or (resi \ d 303 and (name N or name CA or name C or name O or name CB or name CG or name S \ D )) or resid 304 through 330 or (resid 331 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name CE )) or resid 332 through 347 o \ r (resid 348 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 49 through 351 or (resid 352 and (name N or name CA or name C or name O or name \ CB )) or resid 353 through 355 or (resid 356 and (name N or name CA or name C or \ name O or name CB )) or resid 357 through 367 or (resid 368 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 369 through 410 or (re \ sid 411 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 412 through 414 \ or (resid 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 430 or (resid 431 and (name N or name CA or name C or name O or name \ CB )) or resid 432 through 473 or (resid 474 and (name N or name CA or name C o \ r name O or name CB )) or resid 475 through 484 or (resid 485 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name CE )) or resid \ 486 through 493 or (resid 494 through 495 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 496 and (name N or name CA or name C or name O or \ name CB or name CG1 or name CG2)) or (resid 497 through 498 and (name N or name \ CA or name C or name O or name CB )) or resid 499 through 506 or (resid 507 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) or r \ esid 601)) selection = (chain 'E' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD )) or resid 3 through 69 or (resid 70 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2)) or resid 7 \ 1 through 95 or (resid 96 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2)) or resid 97 through 106 or resid 109 through 112 or (r \ esid 113 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name NE )) or resid 114 through 145 or (resid 146 and (name N or name CA \ or name C or name O or name CB )) or resid 147 through 234 or (resid 235 throug \ h 238 and (name N or name CA or name C or name O or name CB )) or resid 239 thro \ ugh 241 or (resid 242 and (name N or name CA or name C or name O or name CB )) o \ r resid 244 through 266 or resid 268 through 290 or resid 293 through 305 or (re \ sid 306 and (name N or name CA or name C or name O or name CB )) or resid 307 th \ rough 324 or (resid 325 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name CE )) or resid 326 through 332 or (resid 333 and (na \ me N or name CA or name C or name O or name CB )) or resid 334 through 350 or (r \ esid 351 through 352 and (name N or name CA or name C or name O or name CB )) or \ resid 353 through 354 or (resid 355 and (name N or name CA or name C or name O \ or name CB or name CG or name CD )) or (resid 356 and (name N or name CA or name \ C or name O or name CB )) or resid 357 through 367 or (resid 368 and (name N or \ name CA or name C or name O or name CB or name CG )) or resid 369 through 414 o \ r (resid 415 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 16 through 427 or (resid 428 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name CE )) or resid 429 through 507 or resid 601)) selection = (chain 'G' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD )) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 4 through 7 or (resid 8 and (name N \ or name CA or name C or name O or name CB )) or resid 9 through 40 or (resid 41 \ and (name N or name CA or name C or name O or name CB )) or resid 42 through 47 \ or (resid 48 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 9 through 50 or (resid 51 and (name N or name CA or name C or name O or name CB \ )) or (resid 52 and (name N or name CA or name C or name O or name CB or name CG \ 1 or name CG2)) or resid 53 through 57 or (resid 58 and (name N or name CA or na \ me C or name O or name CB )) or (resid 59 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD )) or resid 60 through 61 or (resid 62 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ CE )) or resid 63 through 67 or (resid 68 and (name N or name CA or name C or n \ ame O or name CB or name CG )) or resid 69 through 71 or (resid 72 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD or name NE or nam \ e CZ )) or resid 73 through 84 or (resid 85 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name CE )) or resid 86 through 100 or \ (resid 101 through 102 and (name N or name CA or name C or name O or name CB )) \ or resid 103 or (resid 104 and (name N or name CA or name C or name O or name C \ B or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or re \ sid 105 through 106 or (resid 109 through 112 and (name N or name CA or name C o \ r name O or name CB )) or (resid 113 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name NE )) or resid 114 through 122 or (resi \ d 123 and (name N or name CA or name C or name O or name CB )) or resid 124 thro \ ugh 133 or (resid 134 and (name N or name CA or name C or name O or name CB )) o \ r resid 135 through 149 or resid 205 through 207 or (resid 208 and (name N or na \ me CA or name C or name O or name CB )) or resid 209 through 215 or (resid 216 a \ nd (name N or name CA or name C or name O or name CB )) or resid 217 through 232 \ or (resid 233 and (name N or name CA or name C or name O or name CB )) or resid \ 234 through 242 or resid 244 through 247 or (resid 248 and (name N or name CA o \ r name C or name O or name CB or name CG1 or name CG2)) or resid 249 through 262 \ or (resid 263 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE )) or resid 264 through 266 or resid 268 through 302 or (r \ esid 303 and (name N or name CA or name C or name O or name CB or name CG or nam \ e SD )) or resid 304 through 330 or (resid 331 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE )) or resid 332 through 34 \ 7 or (resid 348 and (name N or name CA or name C or name O or name CB )) or resi \ d 349 through 351 or (resid 352 and (name N or name CA or name C or name O or na \ me CB )) or resid 353 through 367 or (resid 368 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 369 through 410 or (resid 411 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD1 or name \ CD2 or name CE1 or name CE2 or name CZ )) or resid 412 through 473 or (resid 474 \ and (name N or name CA or name C or name O or name CB )) or resid 475 through 4 \ 84 or (resid 485 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name CE )) or resid 486 through 493 or (resid 494 through 495 an \ d (name N or name CA or name C or name O or name CB )) or resid 496 through 497 \ or (resid 498 and (name N or name CA or name C or name O or name CB )) or resid \ 499 through 506 or (resid 507 and (name N or name CA or name C or name O or name \ CB or name CG1 or name CG2)) or resid 601)) selection = (chain 'I' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD )) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 4 through 7 or (resid 8 and (name N \ or name CA or name C or name O or name CB )) or resid 9 through 34 or (resid 35 \ and (name N or name CA or name C or name O or name CB or name CG or name CD )) o \ r resid 36 through 40 or (resid 41 and (name N or name CA or name C or name O or \ name CB )) or resid 42 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 50 or (resid 51 and (name N or name \ CA or name C or name O or name CB )) or (resid 52 and (name N or name CA or nam \ e C or name O or name CB or name CG1 or name CG2)) or resid 53 through 57 or (re \ sid 58 and (name N or name CA or name C or name O or name CB )) or (resid 59 and \ (name N or name CA or name C or name O or name CB or name CG or name CD )) or r \ esid 60 through 61 or (resid 62 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name CE )) or resid 63 through 67 or (resid 68 an \ d (name N or name CA or name C or name O or name CB or name CG )) or resid 69 th \ rough 71 or (resid 72 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD or name NE or name CZ )) or resid 73 through 84 or (resid 85 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me CE )) or resid 86 through 100 or (resid 101 through 102 and (name N or name C \ A or name C or name O or name CB )) or resid 103 or (resid 104 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ )) or resid 105 or (resid 106 and (name N or name CA \ or name C or name O or name CB )) or (resid 109 through 112 and (name N or name \ CA or name C or name O or name CB )) or (resid 113 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE )) or resid 114 throug \ h 122 or (resid 123 and (name N or name CA or name C or name O or name CB )) or \ resid 124 through 133 or (resid 134 and (name N or name CA or name C or name O o \ r name CB )) or resid 135 through 144 or (resid 145 through 146 and (name N or n \ ame CA or name C or name O or name CB )) or resid 147 or (resid 148 through 149 \ and (name N or name CA or name C or name O or name CB )) or resid 205 through 20 \ 7 or (resid 208 and (name N or name CA or name C or name O or name CB )) or resi \ d 209 through 215 or (resid 216 and (name N or name CA or name C or name O or na \ me CB )) or resid 217 through 232 or (resid 233 and (name N or name CA or name C \ or name O or name CB )) or resid 234 or (resid 235 through 238 and (name N or n \ ame CA or name C or name O or name CB )) or resid 239 through 242 or resid 244 t \ hrough 247 or (resid 248 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2)) or resid 249 through 262 or (resid 263 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE )) or res \ id 264 through 266 or resid 268 through 290 or resid 293 through 302 or (resid 3 \ 03 and (name N or name CA or name C or name O or name CB or name CG or name SD ) \ ) or resid 304 through 330 or (resid 331 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE )) or resid 332 through 347 or ( \ resid 348 and (name N or name CA or name C or name O or name CB )) or resid 349 \ through 350 or (resid 351 through 352 and (name N or name CA or name C or name O \ or name CB )) or resid 353 through 354 or (resid 355 and (name N or name CA or \ name C or name O or name CB or name CG or name CD )) or (resid 356 and (name N o \ r name CA or name C or name O or name CB )) or resid 357 through 410 or (resid 4 \ 11 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2 or name CE1 or name CE2 or name CZ )) or resid 412 through 473 or (r \ esid 474 and (name N or name CA or name C or name O or name CB )) or resid 475 t \ hrough 484 or (resid 485 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE )) or resid 486 through 493 or (resid 494 throug \ h 495 and (name N or name CA or name C or name O or name CB )) or (resid 496 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) or \ (resid 497 through 498 and (name N or name CA or name C or name O or name CB )) \ or resid 499 through 506 or (resid 507 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2)) or resid 601)) } ncs_group { reference = chain 'M' selection = chain 'S' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain 'N' selection = chain 'T' selection = chain 'V' selection = chain 'Y' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 74.440 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.150 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.004 0.057 30687 Z= 0.174 Angle : 0.643 15.950 42345 Z= 0.356 Chirality : 0.046 0.806 4865 Planarity : 0.009 0.483 4793 Dihedral : 19.165 144.580 11474 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.89 % Favored : 90.99 % Rotamer: Outliers : 0.45 % Allowed : 24.75 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3433 helix: 1.11 (0.16), residues: 1044 sheet: -0.78 (0.21), residues: 692 loop : -2.62 (0.13), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 192 HIS 0.003 0.001 HIS D 358 PHE 0.017 0.001 PHE B 217 TYR 0.020 0.001 TYR I 37 ARG 0.005 0.000 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.18038 ( 1159) hydrogen bonds : angle 7.16383 ( 3385) covalent geometry : bond 0.00354 (30687) covalent geometry : angle 0.64303 (42345) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 207 time to evaluate : 3.382 Fit side-chains REVERT: H 226 GLN cc_start: 0.8274 (mt0) cc_final: 0.7951 (mm-40) REVERT: G 391 SER cc_start: 0.7880 (m) cc_final: 0.7074 (p) outliers start: 8 outliers final: 2 residues processed: 213 average time/residue: 0.3974 time to fit residues: 140.5592 Evaluate side-chains 196 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 194 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain B residue 192 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 319 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 357 GLN I 468 ASN D 320 HIS B 320 HIS ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN F 9 HIS ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.069427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.056691 restraints weight = 89678.328| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.25 r_work: 0.2898 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 30687 Z= 0.217 Angle : 0.636 8.967 42345 Z= 0.342 Chirality : 0.045 0.160 4865 Planarity : 0.005 0.065 4793 Dihedral : 16.049 142.847 5662 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.59 % Favored : 90.38 % Rotamer: Outliers : 3.38 % Allowed : 22.75 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3433 helix: 1.09 (0.16), residues: 1069 sheet: -0.80 (0.20), residues: 700 loop : -2.59 (0.13), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 192 HIS 0.007 0.001 HIS E 360 PHE 0.016 0.002 PHE H 217 TYR 0.018 0.001 TYR H 190 ARG 0.005 0.001 ARG B 361 Details of bonding type rmsd hydrogen bonds : bond 0.05462 ( 1159) hydrogen bonds : angle 5.27928 ( 3385) covalent geometry : bond 0.00505 (30687) covalent geometry : angle 0.63593 (42345) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 203 time to evaluate : 3.057 Fit side-chains REVERT: H 357 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.6879 (mt0) REVERT: I 213 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8113 (mtt180) REVERT: I 281 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8523 (mp) REVERT: D 209 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6672 (mtt90) REVERT: D 219 TRP cc_start: 0.8074 (OUTLIER) cc_final: 0.7801 (m-10) REVERT: B 169 GLU cc_start: 0.7741 (tp30) cc_final: 0.7392 (tp30) REVERT: B 408 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8076 (tt) REVERT: B 414 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8258 (ttp) REVERT: C 281 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8538 (mp) REVERT: F 21 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8494 (tp) REVERT: F 186 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.5897 (ptp-170) outliers start: 80 outliers final: 34 residues processed: 265 average time/residue: 0.4104 time to fit residues: 177.1709 Evaluate side-chains 228 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 357 GLN Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 213 ARG Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 299 CYS Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 194 optimal weight: 3.9990 chunk 119 optimal weight: 0.0870 chunk 330 optimal weight: 0.9980 chunk 322 optimal weight: 3.9990 chunk 318 optimal weight: 1.9990 chunk 286 optimal weight: 0.0870 chunk 268 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 213 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 446 ASN D 163 GLN D 262 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 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 = 0.3318 r_free = 0.3318 target = 0.070919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.058445 restraints weight = 78971.215| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.11 r_work: 0.2949 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30687 Z= 0.127 Angle : 0.563 10.684 42345 Z= 0.301 Chirality : 0.041 0.149 4865 Planarity : 0.005 0.061 4793 Dihedral : 15.910 141.279 5661 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.04 % Favored : 91.93 % Rotamer: Outliers : 2.20 % Allowed : 23.36 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3433 helix: 1.37 (0.16), residues: 1068 sheet: -0.67 (0.20), residues: 699 loop : -2.52 (0.13), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 192 HIS 0.003 0.001 HIS B 320 PHE 0.022 0.001 PHE H 205 TYR 0.016 0.001 TYR F 190 ARG 0.005 0.000 ARG F 382 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 1159) hydrogen bonds : angle 4.88065 ( 3385) covalent geometry : bond 0.00280 (30687) covalent geometry : angle 0.56319 (42345) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 2.951 Fit side-chains REVERT: H 226 GLN cc_start: 0.8444 (mt0) cc_final: 0.8198 (mm-40) REVERT: H 386 ASP cc_start: 0.8442 (m-30) cc_final: 0.8168 (m-30) REVERT: D 209 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6472 (mtt90) REVERT: D 399 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7632 (mt-10) REVERT: B 169 GLU cc_start: 0.7773 (tp30) cc_final: 0.7428 (tp30) REVERT: B 262 GLN cc_start: 0.8087 (mt0) cc_final: 0.7824 (mt0) REVERT: B 314 GLN cc_start: 0.8541 (tt0) cc_final: 0.8258 (tt0) REVERT: B 363 LYS cc_start: 0.8335 (tppt) cc_final: 0.8121 (ttmm) REVERT: B 408 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8000 (tt) REVERT: F 186 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.5773 (ptp-170) REVERT: F 287 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7108 (mtm) outliers start: 51 outliers final: 25 residues processed: 240 average time/residue: 0.3751 time to fit residues: 149.5432 Evaluate side-chains 219 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 111 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 chunk 95 optimal weight: 0.0770 chunk 335 optimal weight: 1.9990 chunk 226 optimal weight: 0.6980 chunk 241 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 227 optimal weight: 0.7980 chunk 276 optimal weight: 0.0670 chunk 285 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 446 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.071435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.058077 restraints weight = 113725.634| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.61 r_work: 0.2926 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30687 Z= 0.116 Angle : 0.542 8.867 42345 Z= 0.289 Chirality : 0.041 0.148 4865 Planarity : 0.004 0.059 4793 Dihedral : 15.821 139.695 5661 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.04 % Favored : 91.93 % Rotamer: Outliers : 3.01 % Allowed : 22.91 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 3433 helix: 1.55 (0.16), residues: 1072 sheet: -0.55 (0.20), residues: 689 loop : -2.46 (0.13), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 192 HIS 0.003 0.001 HIS B 9 PHE 0.020 0.001 PHE B 187 TYR 0.016 0.001 TYR F 190 ARG 0.005 0.000 ARG F 382 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 1159) hydrogen bonds : angle 4.60600 ( 3385) covalent geometry : bond 0.00256 (30687) covalent geometry : angle 0.54158 (42345) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 211 time to evaluate : 3.103 Fit side-chains REVERT: H 386 ASP cc_start: 0.8409 (m-30) cc_final: 0.8100 (m-30) REVERT: I 213 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7950 (mtt180) REVERT: D 179 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8767 (mt) REVERT: D 209 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6403 (mtt90) REVERT: D 399 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7562 (mt-10) REVERT: B 155 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7272 (mm-40) REVERT: B 169 GLU cc_start: 0.7551 (tp30) cc_final: 0.7222 (tp30) REVERT: B 240 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6746 (tpp80) REVERT: B 262 GLN cc_start: 0.7918 (mt0) cc_final: 0.7687 (mt0) REVERT: B 297 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8578 (tmtt) REVERT: B 408 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7881 (tt) REVERT: F 186 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.5848 (ptp-170) REVERT: F 216 THR cc_start: 0.7372 (m) cc_final: 0.6747 (p) REVERT: F 287 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.7050 (mtm) REVERT: G 391 SER cc_start: 0.7688 (t) cc_final: 0.6934 (p) outliers start: 70 outliers final: 38 residues processed: 266 average time/residue: 0.3925 time to fit residues: 171.4689 Evaluate side-chains 237 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 213 ARG Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 470 CYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 215 optimal weight: 3.9990 chunk 315 optimal weight: 0.0970 chunk 218 optimal weight: 0.6980 chunk 319 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 357 GLN E 446 ASN D 358 HIS B 156 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 HIS ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.054733 restraints weight = 108350.096| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.42 r_work: 0.2845 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 30687 Z= 0.266 Angle : 0.656 10.179 42345 Z= 0.347 Chirality : 0.046 0.155 4865 Planarity : 0.005 0.058 4793 Dihedral : 15.906 139.610 5661 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.85 % Favored : 90.09 % Rotamer: Outliers : 4.07 % Allowed : 22.30 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 3433 helix: 1.29 (0.16), residues: 1069 sheet: -0.75 (0.20), residues: 706 loop : -2.50 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 192 HIS 0.010 0.001 HIS E 360 PHE 0.020 0.002 PHE G 245 TYR 0.021 0.002 TYR F 190 ARG 0.006 0.001 ARG F 382 Details of bonding type rmsd hydrogen bonds : bond 0.05679 ( 1159) hydrogen bonds : angle 4.89811 ( 3385) covalent geometry : bond 0.00630 (30687) covalent geometry : angle 0.65587 (42345) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 185 time to evaluate : 2.990 Fit side-chains REVERT: H 199 ASP cc_start: 0.7987 (p0) cc_final: 0.7700 (p0) REVERT: E 330 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8958 (mp) REVERT: D 179 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8832 (mt) REVERT: D 194 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8169 (tt) REVERT: D 209 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6635 (mtt90) REVERT: D 287 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8199 (mtt) REVERT: B 169 GLU cc_start: 0.7926 (tp30) cc_final: 0.7513 (tp30) REVERT: B 297 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8717 (tmtt) REVERT: B 399 GLU cc_start: 0.6884 (mp0) cc_final: 0.6634 (mp0) REVERT: B 408 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8150 (tt) REVERT: C 3 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8072 (tp30) REVERT: F 21 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8508 (tp) REVERT: F 186 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.6096 (ptp-170) REVERT: F 277 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8289 (mtm) REVERT: F 287 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7202 (mtm) outliers start: 96 outliers final: 59 residues processed: 261 average time/residue: 0.3794 time to fit residues: 163.4491 Evaluate side-chains 250 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 179 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 156 GLN Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 380 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 470 CYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 282 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 270 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 208 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 295 optimal weight: 0.0470 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 446 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** 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 = 0.3290 r_free = 0.3290 target = 0.069721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.057035 restraints weight = 92371.702| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.22 r_work: 0.2911 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30687 Z= 0.136 Angle : 0.568 10.955 42345 Z= 0.303 Chirality : 0.042 0.148 4865 Planarity : 0.004 0.058 4793 Dihedral : 15.816 139.793 5661 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.93 % Allowed : 23.40 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.14), residues: 3433 helix: 1.57 (0.16), residues: 1070 sheet: -0.60 (0.20), residues: 708 loop : -2.44 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 192 HIS 0.004 0.001 HIS E 360 PHE 0.020 0.001 PHE B 187 TYR 0.014 0.001 TYR F 190 ARG 0.005 0.000 ARG F 382 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 1159) hydrogen bonds : angle 4.60282 ( 3385) covalent geometry : bond 0.00304 (30687) covalent geometry : angle 0.56779 (42345) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 193 time to evaluate : 3.277 Fit side-chains REVERT: H 199 ASP cc_start: 0.7888 (p0) cc_final: 0.7615 (p0) REVERT: I 222 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.7862 (tp40) REVERT: I 413 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8803 (m) REVERT: D 64 SER cc_start: 0.9347 (OUTLIER) cc_final: 0.9056 (p) REVERT: D 179 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8817 (mt) REVERT: D 209 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6567 (mtt90) REVERT: B 169 GLU cc_start: 0.7856 (tp30) cc_final: 0.7469 (tp30) REVERT: B 205 PHE cc_start: 0.8172 (m-80) cc_final: 0.7905 (m-80) REVERT: B 297 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8631 (tmtt) REVERT: B 408 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8034 (tt) REVERT: C 414 ASP cc_start: 0.8785 (t0) cc_final: 0.8519 (t0) REVERT: F 181 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8119 (m-10) REVERT: F 186 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.5985 (ptp-170) REVERT: F 277 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8239 (mtm) REVERT: F 287 MET cc_start: 0.7349 (mtp) cc_final: 0.7097 (mtm) REVERT: G 391 SER cc_start: 0.8021 (t) cc_final: 0.7323 (p) outliers start: 68 outliers final: 46 residues processed: 246 average time/residue: 0.3838 time to fit residues: 157.5566 Evaluate side-chains 242 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 435 MET Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 380 ASN Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 470 CYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 413 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 149 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 245 optimal weight: 0.9980 chunk 243 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 194 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 262 GLN E 446 ASN D 320 HIS B 156 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.069491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.056103 restraints weight = 126502.300| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.66 r_work: 0.2875 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30687 Z= 0.147 Angle : 0.565 11.082 42345 Z= 0.300 Chirality : 0.042 0.147 4865 Planarity : 0.004 0.058 4793 Dihedral : 15.768 138.693 5661 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.38 % Allowed : 23.40 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3433 helix: 1.67 (0.16), residues: 1071 sheet: -0.60 (0.20), residues: 696 loop : -2.37 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 192 HIS 0.004 0.001 HIS E 360 PHE 0.017 0.001 PHE B 187 TYR 0.015 0.001 TYR D 259 ARG 0.007 0.000 ARG B 382 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 1159) hydrogen bonds : angle 4.54957 ( 3385) covalent geometry : bond 0.00336 (30687) covalent geometry : angle 0.56509 (42345) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 195 time to evaluate : 3.353 Fit side-chains REVERT: H 199 ASP cc_start: 0.7859 (p0) cc_final: 0.7587 (p0) REVERT: I 222 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.7796 (tp40) REVERT: I 413 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8739 (m) REVERT: I 460 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8341 (mp) REVERT: D 64 SER cc_start: 0.9317 (OUTLIER) cc_final: 0.9059 (p) REVERT: D 179 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8794 (mt) REVERT: D 209 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6511 (mtt90) REVERT: B 169 GLU cc_start: 0.7677 (tp30) cc_final: 0.7329 (tp30) REVERT: B 262 GLN cc_start: 0.8026 (mt0) cc_final: 0.7798 (mt0) REVERT: B 297 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8641 (tmtt) REVERT: B 408 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7916 (tt) REVERT: C 3 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7786 (tp30) REVERT: C 123 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8120 (p0) REVERT: C 414 ASP cc_start: 0.8616 (t0) cc_final: 0.8372 (t0) REVERT: F 21 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8391 (tp) REVERT: F 181 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.8030 (m-10) REVERT: F 186 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6010 (ptp-170) REVERT: F 277 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8129 (mtm) REVERT: F 287 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6991 (mtm) REVERT: G 222 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.7889 (tp40) REVERT: G 391 SER cc_start: 0.7872 (t) cc_final: 0.7182 (p) outliers start: 79 outliers final: 52 residues processed: 259 average time/residue: 0.3807 time to fit residues: 164.6726 Evaluate side-chains 253 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 185 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 156 GLN Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 435 MET Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 380 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 470 CYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 413 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 335 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 226 optimal weight: 0.7980 chunk 336 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 262 GLN E 446 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 HIS ** F 370 ASN ** 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 = 0.3272 r_free = 0.3272 target = 0.068891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.056006 restraints weight = 101384.175| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.34 r_work: 0.2882 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30687 Z= 0.184 Angle : 0.585 11.223 42345 Z= 0.311 Chirality : 0.043 0.151 4865 Planarity : 0.005 0.057 4793 Dihedral : 15.781 138.644 5661 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.92 % Favored : 91.05 % Rotamer: Outliers : 3.70 % Allowed : 23.20 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3433 helix: 1.64 (0.16), residues: 1070 sheet: -0.61 (0.20), residues: 697 loop : -2.37 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 192 HIS 0.006 0.001 HIS E 360 PHE 0.019 0.002 PHE B 217 TYR 0.015 0.001 TYR F 190 ARG 0.006 0.000 ARG B 382 Details of bonding type rmsd hydrogen bonds : bond 0.04633 ( 1159) hydrogen bonds : angle 4.60551 ( 3385) covalent geometry : bond 0.00428 (30687) covalent geometry : angle 0.58476 (42345) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 184 time to evaluate : 3.083 Fit side-chains REVERT: H 199 ASP cc_start: 0.7932 (p0) cc_final: 0.7659 (p0) REVERT: I 222 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.7912 (tp40) REVERT: I 460 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8447 (mp) REVERT: D 64 SER cc_start: 0.9362 (OUTLIER) cc_final: 0.9118 (p) REVERT: D 179 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8811 (mt) REVERT: D 209 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6592 (mtt90) REVERT: D 413 LYS cc_start: 0.8840 (mtpp) cc_final: 0.8586 (mttp) REVERT: B 169 GLU cc_start: 0.7930 (tp30) cc_final: 0.7552 (tp30) REVERT: B 205 PHE cc_start: 0.8181 (m-80) cc_final: 0.7954 (m-80) REVERT: B 221 TYR cc_start: 0.5804 (t80) cc_final: 0.5326 (t80) REVERT: B 262 GLN cc_start: 0.8195 (mt0) cc_final: 0.7974 (mt0) REVERT: B 297 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8649 (tmtt) REVERT: B 399 GLU cc_start: 0.6956 (mp0) cc_final: 0.6728 (mp0) REVERT: B 408 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8072 (tt) REVERT: C 3 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7962 (tp30) REVERT: C 414 ASP cc_start: 0.8798 (t0) cc_final: 0.8535 (t0) REVERT: F 21 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8478 (tp) REVERT: F 181 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8070 (m-10) REVERT: F 186 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.6095 (ptp-170) REVERT: F 277 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8442 (mtm) REVERT: F 287 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7090 (mtm) REVERT: G 222 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8003 (tp40) REVERT: G 391 SER cc_start: 0.8056 (t) cc_final: 0.7387 (p) outliers start: 87 outliers final: 59 residues processed: 253 average time/residue: 0.3756 time to fit residues: 157.7610 Evaluate side-chains 258 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 185 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 156 GLN Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 435 MET Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 380 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 470 CYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 413 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 64 optimal weight: 0.6980 chunk 234 optimal weight: 2.9990 chunk 292 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 333 optimal weight: 0.3980 chunk 111 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 272 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 262 GLN E 446 ASN B 156 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** 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 = 0.3288 r_free = 0.3288 target = 0.069610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.056830 restraints weight = 91555.233| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.29 r_work: 0.2903 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30687 Z= 0.141 Angle : 0.566 11.262 42345 Z= 0.300 Chirality : 0.042 0.151 4865 Planarity : 0.004 0.057 4793 Dihedral : 15.735 138.914 5661 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.77 % Favored : 91.20 % Rotamer: Outliers : 3.34 % Allowed : 23.65 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 3433 helix: 1.76 (0.16), residues: 1071 sheet: -0.56 (0.20), residues: 696 loop : -2.34 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 192 HIS 0.004 0.001 HIS E 360 PHE 0.018 0.001 PHE B 217 TYR 0.014 0.001 TYR F 190 ARG 0.006 0.000 ARG F 382 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 1159) hydrogen bonds : angle 4.51370 ( 3385) covalent geometry : bond 0.00320 (30687) covalent geometry : angle 0.56614 (42345) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 187 time to evaluate : 2.978 Fit side-chains REVERT: H 199 ASP cc_start: 0.7893 (p0) cc_final: 0.7620 (p0) REVERT: I 222 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.7871 (tp40) REVERT: I 413 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8754 (m) REVERT: D 64 SER cc_start: 0.9381 (OUTLIER) cc_final: 0.9127 (p) REVERT: D 209 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.6547 (mtt90) REVERT: D 413 LYS cc_start: 0.8792 (mtpp) cc_final: 0.8526 (mttp) REVERT: B 169 GLU cc_start: 0.7935 (tp30) cc_final: 0.7532 (tp30) REVERT: B 205 PHE cc_start: 0.8127 (m-80) cc_final: 0.7883 (m-80) REVERT: B 221 TYR cc_start: 0.5792 (t80) cc_final: 0.5305 (t80) REVERT: B 297 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8653 (tptm) REVERT: B 399 GLU cc_start: 0.6931 (mp0) cc_final: 0.6547 (pm20) REVERT: B 408 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8001 (tt) REVERT: C 3 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7945 (tp30) REVERT: C 123 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8160 (p0) REVERT: C 414 ASP cc_start: 0.8804 (t0) cc_final: 0.8509 (t0) REVERT: F 181 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8118 (m-10) REVERT: F 186 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6136 (ptp-170) REVERT: F 277 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8471 (mtm) REVERT: F 287 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7059 (mtm) REVERT: G 222 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.7982 (tp40) REVERT: G 391 SER cc_start: 0.7996 (t) cc_final: 0.7324 (p) outliers start: 78 outliers final: 57 residues processed: 250 average time/residue: 0.3949 time to fit residues: 167.2194 Evaluate side-chains 255 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 185 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 156 GLN Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 435 MET Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 380 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 470 CYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 413 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 341 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 191 optimal weight: 0.0070 chunk 124 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 chunk 70 optimal weight: 0.4980 chunk 193 optimal weight: 1.9990 chunk 242 optimal weight: 0.0070 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 262 GLN E 446 ASN B 156 GLN B 262 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.071302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.058196 restraints weight = 104348.228| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.48 r_work: 0.2936 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30687 Z= 0.110 Angle : 0.538 10.578 42345 Z= 0.286 Chirality : 0.040 0.150 4865 Planarity : 0.004 0.058 4793 Dihedral : 15.631 138.905 5661 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.56 % Allowed : 24.46 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 3433 helix: 1.96 (0.16), residues: 1068 sheet: -0.45 (0.20), residues: 691 loop : -2.26 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 192 HIS 0.004 0.001 HIS I 207 PHE 0.013 0.001 PHE B 217 TYR 0.016 0.001 TYR B 259 ARG 0.006 0.000 ARG F 382 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 1159) hydrogen bonds : angle 4.33724 ( 3385) covalent geometry : bond 0.00242 (30687) covalent geometry : angle 0.53841 (42345) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 197 time to evaluate : 3.030 Fit side-chains REVERT: H 386 ASP cc_start: 0.8435 (m-30) cc_final: 0.8083 (m-30) REVERT: I 222 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.7782 (tp40) REVERT: I 413 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8676 (m) REVERT: D 64 SER cc_start: 0.9335 (OUTLIER) cc_final: 0.9053 (p) REVERT: D 209 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6330 (mtt90) REVERT: D 290 THR cc_start: 0.8621 (t) cc_final: 0.8359 (m) REVERT: D 329 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8746 (mp) REVERT: D 413 LYS cc_start: 0.8708 (mtpp) cc_final: 0.8476 (mttp) REVERT: B 169 GLU cc_start: 0.7652 (tp30) cc_final: 0.7318 (tp30) REVERT: B 205 PHE cc_start: 0.7986 (m-80) cc_final: 0.7768 (m-80) REVERT: B 221 TYR cc_start: 0.5606 (t80) cc_final: 0.5277 (t80) REVERT: B 399 GLU cc_start: 0.6738 (mp0) cc_final: 0.6479 (pm20) REVERT: B 408 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7863 (tt) REVERT: C 3 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7794 (tp30) REVERT: C 123 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8069 (p0) REVERT: C 414 ASP cc_start: 0.8606 (t0) cc_final: 0.8328 (t0) REVERT: F 181 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8005 (m-10) REVERT: F 186 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6193 (ptp-170) REVERT: G 222 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7874 (tp40) REVERT: G 391 SER cc_start: 0.7684 (t) cc_final: 0.7052 (p) outliers start: 59 outliers final: 42 residues processed: 248 average time/residue: 0.3817 time to fit residues: 158.1886 Evaluate side-chains 241 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 435 MET Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 380 ASN Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 470 CYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 222 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 413 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 76 optimal weight: 0.7980 chunk 317 optimal weight: 5.9990 chunk 301 optimal weight: 2.9990 chunk 261 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 321 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 446 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.070961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.057806 restraints weight = 100481.520| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.50 r_work: 0.2923 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30687 Z= 0.117 Angle : 0.538 10.320 42345 Z= 0.285 Chirality : 0.041 0.148 4865 Planarity : 0.004 0.058 4793 Dihedral : 15.560 137.877 5661 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.73 % Allowed : 24.54 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.15), residues: 3433 helix: 1.99 (0.16), residues: 1070 sheet: -0.40 (0.20), residues: 695 loop : -2.22 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 192 HIS 0.003 0.001 HIS I 207 PHE 0.022 0.001 PHE B 187 TYR 0.018 0.001 TYR D 259 ARG 0.006 0.000 ARG F 276 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 1159) hydrogen bonds : angle 4.32343 ( 3385) covalent geometry : bond 0.00259 (30687) covalent geometry : angle 0.53838 (42345) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16792.95 seconds wall clock time: 290 minutes 53.59 seconds (17453.59 seconds total)