Starting phenix.real_space_refine on Thu Oct 29 04:17:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6udq_20743/10_2026/6udq_20743.cif Found real_map, /net/cci-nas-00/data/ceres_data/6udq_20743/10_2026/6udq_20743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6udq_20743/10_2026/6udq_20743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6udq_20743/10_2026/6udq_20743.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6udq_20743/10_2026/6udq_20743.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6udq_20743/10_2026/6udq_20743.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6udq_20743/10_2026/6udq_20743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6udq_20743/10_2026/6udq_20743.map" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.059 sd= 3.203 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 80 5.49 5 S 172 5.16 5 C 19292 2.51 5 N 5324 2.21 5 O 6140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31008 Number of models: 1 Model: "" Number of chains: 20 Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "A" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "E" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "B" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "F" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "K" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "C" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "G" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "D" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "H" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "A" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 149 Unusual residues: {'ATP': 2, 'GTP': 2} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'GTP': 2} Classifications: {'RNAv2': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna2p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 149 Unusual residues: {'ATP': 2, 'GTP': 2} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'GTP': 2} Classifications: {'RNAv2': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Chain: "D" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 6.64, per 1000 atoms: 0.21 Number of scatterers: 31008 At special positions: 0 Unit cell: (151.25, 152.076, 116.537, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 172 16.00 P 80 15.00 O 6140 8.00 N 5324 7.00 C 19292 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.4 seconds 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 45 sheets defined 38.2% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'I' and resid 1 through 6 removed outlier: 3.774A pdb=" N ILE I 6 " --> pdb=" O ALA I 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.525A pdb=" N GLN A 48 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.602A pdb=" N ALA A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.639A pdb=" N VAL A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.043A pdb=" N ILE A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 164' Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 193 through 204 Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.677A pdb=" N ARG A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 256 through 267 Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.909A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.969A pdb=" N ALA A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 355 removed outlier: 3.671A pdb=" N TYR A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 3.898A pdb=" N ILE A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 486 Processing helix chain 'A' and resid 496 through 502 removed outlier: 3.593A pdb=" N GLY A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 25 removed outlier: 3.691A pdb=" N ASN E 25 " --> pdb=" O GLN E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.636A pdb=" N GLN E 48 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL E 49 " --> pdb=" O ALA E 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 45 through 49' Processing helix chain 'E' and resid 75 through 85 removed outlier: 3.548A pdb=" N ALA E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 107 Processing helix chain 'E' and resid 127 through 137 removed outlier: 3.754A pdb=" N PHE E 131 " --> pdb=" O VAL E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 193 through 204 Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 256 through 267 removed outlier: 3.614A pdb=" N GLN E 265 " --> pdb=" O ASP E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.985A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 removed outlier: 3.900A pdb=" N ALA E 310 " --> pdb=" O THR E 306 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 311 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 355 removed outlier: 3.773A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.734A pdb=" N ILE E 373 " --> pdb=" O ASN E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 486 Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 84 removed outlier: 3.609A pdb=" N ALA B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 126 through 138 removed outlier: 3.657A pdb=" N VAL B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.529A pdb=" N GLU B 177 " --> pdb=" O PHE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 193 through 204 removed outlier: 3.538A pdb=" N ALA B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.517A pdb=" N ARG B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 256 through 267 Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.874A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.958A pdb=" N ALA B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.791A pdb=" N TYR B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 378 removed outlier: 3.947A pdb=" N ILE B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 486 Processing helix chain 'B' and resid 496 through 502 removed outlier: 3.833A pdb=" N GLY B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 25 removed outlier: 3.656A pdb=" N ASN F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 removed outlier: 3.526A pdb=" N GLN F 48 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL F 49 " --> pdb=" O ALA F 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 45 through 49' Processing helix chain 'F' and resid 75 through 85 removed outlier: 3.524A pdb=" N ALA F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 108 removed outlier: 3.539A pdb=" N GLU F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS F 108 " --> pdb=" O VAL F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.697A pdb=" N PHE F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 178 removed outlier: 3.750A pdb=" N GLU F 177 " --> pdb=" O PHE F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 185 No H-bonds generated for 'chain 'F' and resid 183 through 185' Processing helix chain 'F' and resid 193 through 204 Processing helix chain 'F' and resid 224 through 233 Processing helix chain 'F' and resid 255 through 267 removed outlier: 4.133A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN F 265 " --> pdb=" O ASP F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 removed outlier: 3.978A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 removed outlier: 3.881A pdb=" N ALA F 310 " --> pdb=" O THR F 306 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS F 311 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 355 removed outlier: 3.622A pdb=" N TYR F 348 " --> pdb=" O ALA F 344 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.666A pdb=" N ILE F 373 " --> pdb=" O ASN F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 486 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'K' and resid 2 through 6 removed outlier: 3.774A pdb=" N ILE K 6 " --> pdb=" O ALA K 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 2 through 6' Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 84 removed outlier: 3.576A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 126 through 138 removed outlier: 3.866A pdb=" N VAL C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 removed outlier: 3.694A pdb=" N GLU C 177 " --> pdb=" O PHE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 193 through 204 removed outlier: 3.664A pdb=" N ALA C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 removed outlier: 3.543A pdb=" N ARG C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 267 Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.894A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.972A pdb=" N ALA C 310 " --> pdb=" O THR C 306 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 342 through 355 removed outlier: 3.731A pdb=" N TYR C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 378 removed outlier: 3.916A pdb=" N ILE C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 472 Processing helix chain 'C' and resid 475 through 486 Processing helix chain 'C' and resid 496 through 502 removed outlier: 3.507A pdb=" N GLY C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 removed outlier: 3.673A pdb=" N GLN G 48 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL G 49 " --> pdb=" O ALA G 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 49' Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.555A pdb=" N ALA G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 removed outlier: 3.711A pdb=" N LYS G 108 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 137 removed outlier: 3.645A pdb=" N PHE G 131 " --> pdb=" O VAL G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 185 No H-bonds generated for 'chain 'G' and resid 183 through 185' Processing helix chain 'G' and resid 193 through 204 Processing helix chain 'G' and resid 224 through 233 Processing helix chain 'G' and resid 255 through 267 removed outlier: 4.135A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN G 265 " --> pdb=" O ASP G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 removed outlier: 3.899A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 315 removed outlier: 3.890A pdb=" N ALA G 310 " --> pdb=" O THR G 306 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS G 311 " --> pdb=" O ALA G 307 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 342 through 355 removed outlier: 3.817A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 removed outlier: 3.864A pdb=" N ILE G 373 " --> pdb=" O ASN G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 486 Processing helix chain 'G' and resid 494 through 502 removed outlier: 3.660A pdb=" N GLY G 502 " --> pdb=" O GLN G 498 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.802A pdb=" N ILE L 6 " --> pdb=" O ALA L 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2 through 6' Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 84 removed outlier: 3.659A pdb=" N ALA D 81 " --> pdb=" O GLY D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 126 through 138 removed outlier: 3.839A pdb=" N VAL D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE D 131 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.599A pdb=" N GLU D 177 " --> pdb=" O PHE D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 193 through 204 removed outlier: 3.765A pdb=" N ALA D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.681A pdb=" N ARG D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 267 removed outlier: 3.770A pdb=" N GLN D 265 " --> pdb=" O ASP D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.919A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.975A pdb=" N ALA D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 355 removed outlier: 3.668A pdb=" N TYR D 348 " --> pdb=" O ALA D 344 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 378 removed outlier: 3.928A pdb=" N ILE D 373 " --> pdb=" O ASN D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 486 Processing helix chain 'D' and resid 496 through 502 removed outlier: 3.587A pdb=" N GLY D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 removed outlier: 3.630A pdb=" N VAL H 49 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 85 removed outlier: 3.639A pdb=" N ALA H 81 " --> pdb=" O GLY H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 108 Processing helix chain 'H' and resid 128 through 137 Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'H' and resid 193 through 204 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 255 through 267 removed outlier: 4.134A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN H 265 " --> pdb=" O ASP H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 removed outlier: 3.535A pdb=" N ILE H 284 " --> pdb=" O SER H 280 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 315 removed outlier: 3.886A pdb=" N ALA H 310 " --> pdb=" O THR H 306 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS H 311 " --> pdb=" O ALA H 307 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 342 through 355 removed outlier: 3.661A pdb=" N TYR H 348 " --> pdb=" O ALA H 344 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 removed outlier: 3.716A pdb=" N ILE H 373 " --> pdb=" O ASN H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 486 Processing helix chain 'H' and resid 494 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.791A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLY A 89 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA A 249 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.054A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 209 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE A 221 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE A 211 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 Processing sheet with id=AA7, first strand: chain 'A' and resid 510 through 511 Processing sheet with id=AA8, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AA9, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.647A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E 299 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 142 through 145 Processing sheet with id=AB2, first strand: chain 'E' and resid 188 through 189 removed outlier: 5.668A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AB4, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB5, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.763A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLY B 89 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ALA B 249 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.564A pdb=" N ILE B 157 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 188 through 189 removed outlier: 5.925A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU B 209 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE B 221 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 211 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 401 through 402 Processing sheet with id=AB9, first strand: chain 'B' and resid 510 through 511 Processing sheet with id=AC1, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC2, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'F' and resid 66 through 67 removed outlier: 6.671A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL F 299 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ARG F 322 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLY F 301 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE F 91 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 142 through 145 Processing sheet with id=AC5, first strand: chain 'F' and resid 209 through 212 removed outlier: 3.527A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 508 through 510 removed outlier: 4.336A pdb=" N SER F 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.759A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLY C 89 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ALA C 249 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.530A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 188 through 189 removed outlier: 5.557A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU C 209 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE C 221 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 211 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 401 through 403 Processing sheet with id=AD4, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AD5, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.669A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 142 through 145 Processing sheet with id=AD7, first strand: chain 'G' and resid 209 through 212 Processing sheet with id=AD8, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AD9, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AE1, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.763A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLY D 89 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ALA D 249 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.621A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE D 157 " --> pdb=" O THR D 180 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR D 180 " --> pdb=" O ILE D 157 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 188 through 189 removed outlier: 5.860A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU D 209 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE D 221 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE D 211 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 401 through 402 Processing sheet with id=AE5, first strand: chain 'D' and resid 510 through 511 Processing sheet with id=AE6, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE7, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.659A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL H 299 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 142 through 145 Processing sheet with id=AE9, first strand: chain 'H' and resid 188 through 189 removed outlier: 5.580A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 1025 hydrogen bonds defined for protein. 2913 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5227 1.31 - 1.43: 7594 1.43 - 1.56: 18260 1.56 - 1.69: 167 1.69 - 1.82: 280 Bond restraints: 31528 Sorted by residual: bond pdb=" C2' GTP C 602 " pdb=" C3' GTP C 602 " ideal model delta sigma weight residual 1.524 1.228 0.296 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C2' GTP D 602 " pdb=" C3' GTP D 602 " ideal model delta sigma weight residual 1.524 1.228 0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C2' GTP B 602 " pdb=" C3' GTP B 602 " ideal model delta sigma weight residual 1.524 1.228 0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C2' GTP A 602 " pdb=" C3' GTP A 602 " ideal model delta sigma weight residual 1.524 1.229 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C2' GTP E 602 " pdb=" C3' GTP E 602 " ideal model delta sigma weight residual 1.524 1.229 0.295 2.00e-02 2.50e+03 2.17e+02 ... (remaining 31523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.06: 42192 4.06 - 8.13: 475 8.13 - 12.19: 74 12.19 - 16.26: 4 16.26 - 20.32: 11 Bond angle restraints: 42756 Sorted by residual: angle pdb=" PB ATP A 605 " pdb=" O3B ATP A 605 " pdb=" PG ATP A 605 " ideal model delta sigma weight residual 139.87 119.55 20.32 1.00e+00 1.00e+00 4.13e+02 angle pdb=" PB ATP C 605 " pdb=" O3B ATP C 605 " pdb=" PG ATP C 605 " ideal model delta sigma weight residual 139.87 119.57 20.30 1.00e+00 1.00e+00 4.12e+02 angle pdb=" PB ATP B 604 " pdb=" O3B ATP B 604 " pdb=" PG ATP B 604 " ideal model delta sigma weight residual 139.87 119.80 20.07 1.00e+00 1.00e+00 4.03e+02 angle pdb=" PB ATP F 604 " pdb=" O3B ATP F 604 " pdb=" PG ATP F 604 " ideal model delta sigma weight residual 139.87 119.93 19.94 1.00e+00 1.00e+00 3.97e+02 angle pdb=" PB ATP A 604 " pdb=" O3B ATP A 604 " pdb=" PG ATP A 604 " ideal model delta sigma weight residual 139.87 120.64 19.23 1.00e+00 1.00e+00 3.70e+02 ... (remaining 42751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 18585 35.48 - 70.97: 209 70.97 - 106.45: 25 106.45 - 141.94: 32 141.94 - 177.42: 17 Dihedral angle restraints: 18868 sinusoidal: 7628 harmonic: 11240 Sorted by residual: dihedral pdb=" CA SER L 11 " pdb=" C SER L 11 " pdb=" N TYR L 12 " pdb=" CA TYR L 12 " ideal model delta harmonic sigma weight residual 180.00 134.87 45.13 0 5.00e+00 4.00e-02 8.15e+01 dihedral pdb=" CA SER I 11 " pdb=" C SER I 11 " pdb=" N TYR I 12 " pdb=" CA TYR I 12 " ideal model delta harmonic sigma weight residual 180.00 134.95 45.05 0 5.00e+00 4.00e-02 8.12e+01 dihedral pdb=" CA SER J 11 " pdb=" C SER J 11 " pdb=" N TYR J 12 " pdb=" CA TYR J 12 " ideal model delta harmonic sigma weight residual 180.00 135.50 44.50 0 5.00e+00 4.00e-02 7.92e+01 ... (remaining 18865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3418 0.056 - 0.113: 1110 0.113 - 0.169: 281 0.169 - 0.226: 42 0.226 - 0.282: 17 Chirality restraints: 4868 Sorted by residual: chirality pdb=" C2' IMP B 601 " pdb=" C1' IMP B 601 " pdb=" C3' IMP B 601 " pdb=" O2' IMP B 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C2' IMP E 601 " pdb=" C1' IMP E 601 " pdb=" C3' IMP E 601 " pdb=" O2' IMP E 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C2' IMP C 601 " pdb=" C1' IMP C 601 " pdb=" C3' IMP C 601 " pdb=" O2' IMP C 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 4865 not shown) Planarity restraints: 5360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU H 169 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C GLU H 169 " -0.045 2.00e-02 2.50e+03 pdb=" O GLU H 169 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU H 170 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 169 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" C GLU E 169 " 0.041 2.00e-02 2.50e+03 pdb=" O GLU E 169 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU E 170 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 169 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C GLU F 169 " 0.039 2.00e-02 2.50e+03 pdb=" O GLU F 169 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU F 170 " -0.013 2.00e-02 2.50e+03 ... (remaining 5357 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6150 2.77 - 3.30: 27811 3.30 - 3.84: 52022 3.84 - 4.37: 63049 4.37 - 4.90: 106262 Nonbonded interactions: 255294 Sorted by model distance: nonbonded pdb=" OG1 THR C 193 " pdb=" OE1 GLU C 196 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR B 193 " pdb=" OE1 GLU B 196 " model vdw 2.248 3.040 nonbonded pdb=" OD1 ASP C 146 " pdb=" OG SER C 152 " model vdw 2.249 3.040 nonbonded pdb=" OG1 THR D 193 " pdb=" OE1 GLU D 196 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP D 146 " pdb=" OG SER D 152 " model vdw 2.268 3.040 ... (remaining 255289 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 12 through 603) selection = (chain 'B' and resid 12 through 603) selection = (chain 'C' and resid 12 through 603) selection = (chain 'D' and resid 12 through 603) selection = (chain 'E' and resid 12 through 603) selection = (chain 'F' and resid 12 through 603) selection = (chain 'G' and resid 12 through 603) selection = (chain 'H' and resid 12 through 603) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 28.350 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 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 : 0.014 0.296 31534 Z= 0.698 Angle : 1.203 20.322 42756 Z= 0.726 Chirality : 0.061 0.282 4868 Planarity : 0.006 0.056 5360 Dihedral : 14.709 177.420 11692 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.09 % Allowed : 3.75 % Favored : 95.16 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 1.52 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.91 (0.11), residues: 3916 helix: -3.28 (0.09), residues: 1348 sheet: -2.22 (0.20), residues: 544 loop : -2.14 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG C 407 TYR 0.038 0.003 TYR F 400 PHE 0.026 0.003 PHE A 401 HIS 0.006 0.001 HIS H 466 Details of bonding type rmsd/Z covalent geometry : bond 0.01380 / 0.70 (31528) covalent geometry : angle 1.20274 / 0.73 (42756) hydrogen bonds : bond 0.20435 / 13.44 ( 1025) hydrogen bonds : angle 7.96785 / 5.44 ( 2913) Misc. bond : bond 0.00190 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 809 time to evaluate : 1.080 Fit side-chains REVERT: A 34 ASP cc_start: 0.8493 (m-30) cc_final: 0.8190 (m-30) REVERT: A 116 THR cc_start: 0.8543 (m) cc_final: 0.8248 (m) REVERT: A 179 MET cc_start: 0.8173 (pp-130) cc_final: 0.7565 (pp-130) REVERT: A 512 ARG cc_start: 0.7007 (ttt-90) cc_final: 0.6280 (tpt90) REVERT: E 124 LYS cc_start: 0.7358 (tppt) cc_final: 0.6981 (tptp) REVERT: E 206 LYS cc_start: 0.7328 (tppp) cc_final: 0.7050 (tptp) REVERT: E 265 GLN cc_start: 0.8620 (tt0) cc_final: 0.8351 (mt0) REVERT: E 330 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9071 (pp) REVERT: E 352 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8347 (tm-30) REVERT: E 412 ARG cc_start: 0.8117 (ptt-90) cc_final: 0.7655 (ptt180) REVERT: E 438 LYS cc_start: 0.7705 (mtmm) cc_final: 0.7257 (mttm) REVERT: B 116 THR cc_start: 0.8528 (m) cc_final: 0.8254 (m) REVERT: B 119 VAL cc_start: 0.8445 (m) cc_final: 0.8221 (p) REVERT: B 152 SER cc_start: 0.6602 (t) cc_final: 0.6247 (t) REVERT: B 179 MET cc_start: 0.8301 (pp-130) cc_final: 0.7546 (ppp) REVERT: B 181 LYS cc_start: 0.7406 (mppt) cc_final: 0.7202 (mmmt) REVERT: F 179 MET cc_start: 0.8191 (ppp) cc_final: 0.7807 (ppp) REVERT: F 265 GLN cc_start: 0.8678 (tt0) cc_final: 0.8168 (mt0) REVERT: F 330 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8831 (pp) REVERT: F 412 ARG cc_start: 0.8015 (ptt-90) cc_final: 0.7740 (ptt180) REVERT: C 59 ILE cc_start: 0.8588 (mm) cc_final: 0.8380 (mt) REVERT: C 82 MET cc_start: 0.8964 (mmm) cc_final: 0.8577 (mmt) REVERT: C 152 SER cc_start: 0.7041 (t) cc_final: 0.6810 (t) REVERT: C 192 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7456 (tp) REVERT: C 512 ARG cc_start: 0.6815 (ttt-90) cc_final: 0.6164 (tpt90) REVERT: G 109 LYS cc_start: 0.8380 (mtpt) cc_final: 0.7728 (mttt) REVERT: G 179 MET cc_start: 0.8324 (ppp) cc_final: 0.8001 (ppp) REVERT: G 206 LYS cc_start: 0.7725 (tptt) cc_final: 0.7500 (tppt) REVERT: G 265 GLN cc_start: 0.8689 (tt0) cc_final: 0.8320 (mt0) REVERT: G 330 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.8938 (pp) REVERT: G 411 TYR cc_start: 0.9065 (t80) cc_final: 0.8704 (t80) REVERT: G 412 ARG cc_start: 0.7922 (ptt-90) cc_final: 0.7564 (ptt180) REVERT: G 480 ARG cc_start: 0.8766 (mtm-85) cc_final: 0.8565 (mtm-85) REVERT: D 179 MET cc_start: 0.8079 (pp-130) cc_final: 0.7683 (pp-130) REVERT: D 192 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7478 (tp) REVERT: H 94 ASN cc_start: 0.8842 (t0) cc_final: 0.8431 (t0) REVERT: H 124 LYS cc_start: 0.7361 (tppt) cc_final: 0.6944 (tptp) REVERT: H 179 MET cc_start: 0.8312 (ppp) cc_final: 0.7692 (ppp) REVERT: H 184 ASP cc_start: 0.7958 (p0) cc_final: 0.7455 (p0) REVERT: H 265 GLN cc_start: 0.8759 (tt0) cc_final: 0.8147 (mt0) REVERT: H 330 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8866 (pp) REVERT: H 412 ARG cc_start: 0.8171 (ptt-90) cc_final: 0.7750 (ptt180) outliers start: 35 outliers final: 6 residues processed: 820 average time/residue: 0.2101 time to fit residues: 267.3139 Evaluate side-chains 553 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 541 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 330 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.0570 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 HIS ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS E 253 HIS E 368 GLN E 448 GLN B 202 GLN B 253 HIS ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 441 GLN B 466 HIS B 469 GLN F 94 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN F 466 HIS C 48 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN C 466 HIS G 94 ASN G 102 ASN G 253 HIS G 303 ASN G 507 HIS D 21 GLN D 253 HIS ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN D 466 HIS H 94 ASN H 102 ASN H 112 GLN H 253 HIS ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 368 GLN H 466 HIS H 504 HIS H 507 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.153210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122252 restraints weight = 38468.977| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.30 r_work: 0.3202 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31534 Z= 0.133 Angle : 0.640 8.618 42756 Z= 0.316 Chirality : 0.046 0.211 4868 Planarity : 0.004 0.046 5360 Dihedral : 16.870 173.864 4587 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.79 % Allowed : 10.48 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.12), residues: 3916 helix: -1.44 (0.12), residues: 1348 sheet: -1.68 (0.22), residues: 520 loop : -1.54 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 512 TYR 0.013 0.001 TYR F 400 PHE 0.017 0.001 PHE F 99 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (31528) covalent geometry : angle 0.64014 / 0.32 (42756) hydrogen bonds : bond 0.03607 / 2.37 ( 1025) hydrogen bonds : angle 5.47061 / 3.81 ( 2913) Misc. bond : bond 0.00090 / 0.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 594 time to evaluate : 0.907 Fit side-chains REVERT: A 28 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8194 (t0) REVERT: A 119 VAL cc_start: 0.8427 (m) cc_final: 0.8220 (p) REVERT: A 192 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7588 (tp) REVERT: A 238 LYS cc_start: 0.8593 (mtmm) cc_final: 0.8372 (mttt) REVERT: E 94 ASN cc_start: 0.9313 (t0) cc_final: 0.8846 (t0) REVERT: E 124 LYS cc_start: 0.7501 (tppt) cc_final: 0.7106 (tptp) REVERT: E 179 MET cc_start: 0.8658 (ppp) cc_final: 0.8318 (ppp) REVERT: E 184 ASP cc_start: 0.8140 (p0) cc_final: 0.7615 (p0) REVERT: E 265 GLN cc_start: 0.8847 (tt0) cc_final: 0.8372 (mt0) REVERT: E 330 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9047 (pp) REVERT: E 352 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8732 (tm-30) REVERT: E 412 ARG cc_start: 0.7864 (ptt-90) cc_final: 0.7312 (ptt180) REVERT: E 420 MET cc_start: 0.5768 (mpp) cc_final: 0.5405 (mpp) REVERT: E 438 LYS cc_start: 0.7541 (mtmm) cc_final: 0.7010 (mttm) REVERT: B 181 LYS cc_start: 0.7280 (mppt) cc_final: 0.7030 (mmmt) REVERT: B 274 ASP cc_start: 0.9093 (t70) cc_final: 0.8826 (t0) REVERT: B 343 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6838 (tt0) REVERT: F 50 ASP cc_start: 0.8713 (t0) cc_final: 0.8509 (t0) REVERT: F 94 ASN cc_start: 0.9341 (t160) cc_final: 0.8977 (t0) REVERT: F 109 LYS cc_start: 0.8011 (mttt) cc_final: 0.7627 (mttt) REVERT: F 179 MET cc_start: 0.8628 (ppp) cc_final: 0.8265 (ppp) REVERT: F 184 ASP cc_start: 0.8296 (p0) cc_final: 0.7785 (p0) REVERT: F 254 GLU cc_start: 0.8302 (mp0) cc_final: 0.8062 (mp0) REVERT: F 265 GLN cc_start: 0.8857 (tt0) cc_final: 0.8199 (mt0) REVERT: F 330 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.8941 (pp) REVERT: F 352 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8734 (tm-30) REVERT: F 412 ARG cc_start: 0.7663 (ptt-90) cc_final: 0.7289 (ptt180) REVERT: C 59 ILE cc_start: 0.8471 (mm) cc_final: 0.8222 (mt) REVERT: C 179 MET cc_start: 0.7916 (pp-130) cc_final: 0.7122 (pp-130) REVERT: C 192 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7402 (tp) REVERT: C 206 LYS cc_start: 0.8012 (mmmm) cc_final: 0.7798 (mmmm) REVERT: C 216 ASP cc_start: 0.7928 (m-30) cc_final: 0.7497 (t0) REVERT: C 388 SER cc_start: 0.9124 (p) cc_final: 0.8896 (p) REVERT: G 36 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8368 (pp) REVERT: G 94 ASN cc_start: 0.9312 (t160) cc_final: 0.8953 (t0) REVERT: G 109 LYS cc_start: 0.8570 (mtpt) cc_final: 0.7944 (mttt) REVERT: G 179 MET cc_start: 0.8485 (ppp) cc_final: 0.7830 (ppp) REVERT: G 265 GLN cc_start: 0.8895 (tt0) cc_final: 0.8385 (mt0) REVERT: G 330 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.8862 (pp) REVERT: G 412 ARG cc_start: 0.7584 (ptt-90) cc_final: 0.7036 (ptt180) REVERT: G 420 MET cc_start: 0.5569 (mpp) cc_final: 0.5180 (mpp) REVERT: D 103 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: D 179 MET cc_start: 0.8147 (pp-130) cc_final: 0.7283 (pp-130) REVERT: D 192 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7300 (tp) REVERT: H 36 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8257 (pp) REVERT: H 94 ASN cc_start: 0.9306 (t160) cc_final: 0.8897 (t0) REVERT: H 159 SER cc_start: 0.9185 (m) cc_final: 0.8287 (t) REVERT: H 179 MET cc_start: 0.8539 (ppp) cc_final: 0.7612 (ppp) REVERT: H 184 ASP cc_start: 0.8157 (p0) cc_final: 0.7756 (p0) REVERT: H 252 THR cc_start: 0.9201 (p) cc_final: 0.8926 (p) REVERT: H 265 GLN cc_start: 0.8860 (tt0) cc_final: 0.8174 (mt0) REVERT: H 330 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8912 (pp) REVERT: H 412 ARG cc_start: 0.7830 (ptt-90) cc_final: 0.7304 (ptt180) outliers start: 90 outliers final: 38 residues processed: 648 average time/residue: 0.1869 time to fit residues: 196.9206 Evaluate side-chains 545 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 495 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 482 MET Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 482 MET Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 368 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [212, 287, 146, 213, 292, 243, 331, 158, 22, 11, 92] chunk 212 optimal weight: 0.0040 chunk 287 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 213 optimal weight: 0.6980 chunk 292 optimal weight: 0.0470 chunk 243 optimal weight: 4.9990 chunk 331 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.5292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN A 469 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 507 HIS C 171 HIS ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 HIS ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN H 112 GLN H 253 HIS H 334 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.154543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.123414 restraints weight = 38400.783| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.33 r_work: 0.3254 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31534 Z= 0.113 Angle : 0.594 8.214 42756 Z= 0.289 Chirality : 0.045 0.176 4868 Planarity : 0.003 0.038 5360 Dihedral : 16.190 171.579 4586 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.88 % Allowed : 12.69 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.13), residues: 3916 helix: -0.48 (0.14), residues: 1356 sheet: -1.27 (0.24), residues: 456 loop : -1.36 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 480 TYR 0.017 0.001 TYR H 509 PHE 0.011 0.001 PHE D 401 HIS 0.007 0.001 HIS F 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (31528) covalent geometry : angle 0.59368 / 0.29 (42756) hydrogen bonds : bond 0.02970 / 1.96 ( 1025) hydrogen bonds : angle 5.03915 / 3.53 ( 2913) Misc. bond : bond 0.00248 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 557 time to evaluate : 1.369 Fit side-chains REVERT: A 28 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8144 (t0) REVERT: A 150 MET cc_start: 0.7431 (mmm) cc_final: 0.6863 (tpt) REVERT: A 175 LEU cc_start: 0.8616 (mp) cc_final: 0.8318 (mp) REVERT: A 179 MET cc_start: 0.8197 (pp-130) cc_final: 0.7155 (pp-130) REVERT: A 192 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7622 (tp) REVERT: A 438 LYS cc_start: 0.7695 (ptmt) cc_final: 0.6467 (tptm) REVERT: A 513 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6606 (mp) REVERT: E 94 ASN cc_start: 0.9289 (t0) cc_final: 0.8859 (t0) REVERT: E 124 LYS cc_start: 0.7485 (tppt) cc_final: 0.7054 (tptp) REVERT: E 149 ARG cc_start: 0.7758 (mtm-85) cc_final: 0.7159 (mtp85) REVERT: E 179 MET cc_start: 0.8611 (ppp) cc_final: 0.8125 (ppp) REVERT: E 184 ASP cc_start: 0.8031 (p0) cc_final: 0.7555 (p0) REVERT: E 185 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7072 (mp) REVERT: E 224 ARG cc_start: 0.8321 (ttt90) cc_final: 0.8070 (ttt-90) REVERT: E 265 GLN cc_start: 0.8837 (tt0) cc_final: 0.8454 (mt0) REVERT: E 330 ILE cc_start: 0.9469 (OUTLIER) cc_final: 0.9189 (pp) REVERT: E 352 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8846 (tm-30) REVERT: E 368 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7671 (mp-120) REVERT: E 412 ARG cc_start: 0.8028 (ptt-90) cc_final: 0.7528 (ptt180) REVERT: E 420 MET cc_start: 0.5669 (mpp) cc_final: 0.5278 (mpp) REVERT: E 438 LYS cc_start: 0.7650 (mtmm) cc_final: 0.6964 (mttp) REVERT: B 28 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8030 (t0) REVERT: B 199 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7208 (pt0) REVERT: B 274 ASP cc_start: 0.9101 (t70) cc_final: 0.8860 (t0) REVERT: B 410 LYS cc_start: 0.7685 (ttmm) cc_final: 0.7006 (mmtt) REVERT: F 94 ASN cc_start: 0.9326 (t160) cc_final: 0.8909 (t0) REVERT: F 109 LYS cc_start: 0.8219 (mttt) cc_final: 0.7724 (mttt) REVERT: F 128 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7363 (mmt90) REVERT: F 179 MET cc_start: 0.8471 (ppp) cc_final: 0.8174 (ppp) REVERT: F 184 ASP cc_start: 0.8170 (p0) cc_final: 0.7687 (p0) REVERT: F 254 GLU cc_start: 0.8312 (mp0) cc_final: 0.8078 (mp0) REVERT: F 265 GLN cc_start: 0.8893 (tt0) cc_final: 0.8306 (mt0) REVERT: F 352 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8314 (tm-30) REVERT: F 412 ARG cc_start: 0.7875 (ptt-90) cc_final: 0.7342 (ptt180) REVERT: C 179 MET cc_start: 0.8146 (pp-130) cc_final: 0.7346 (pp-130) REVERT: C 192 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7430 (tp) REVERT: C 206 LYS cc_start: 0.7873 (mmmm) cc_final: 0.7584 (mmmm) REVERT: C 404 ASP cc_start: 0.5952 (t0) cc_final: 0.5669 (t0) REVERT: C 498 GLN cc_start: 0.6108 (OUTLIER) cc_final: 0.5845 (mt0) REVERT: G 94 ASN cc_start: 0.9292 (t160) cc_final: 0.9078 (t0) REVERT: G 179 MET cc_start: 0.8524 (ppp) cc_final: 0.7936 (ppp) REVERT: G 265 GLN cc_start: 0.8888 (tt0) cc_final: 0.8470 (mt0) REVERT: G 330 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.8958 (pp) REVERT: G 412 ARG cc_start: 0.7607 (ptt-90) cc_final: 0.7113 (ptt180) REVERT: G 420 MET cc_start: 0.5642 (mpp) cc_final: 0.5421 (mpp) REVERT: D 103 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: D 126 ARG cc_start: 0.6858 (mtt-85) cc_final: 0.4540 (mtt-85) REVERT: D 179 MET cc_start: 0.8297 (pp-130) cc_final: 0.7360 (pp-130) REVERT: D 192 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7304 (tp) REVERT: D 274 ASP cc_start: 0.9120 (t70) cc_final: 0.8889 (t0) REVERT: D 410 LYS cc_start: 0.7626 (ttmm) cc_final: 0.7329 (mtpp) REVERT: H 94 ASN cc_start: 0.9294 (t160) cc_final: 0.8831 (t0) REVERT: H 159 SER cc_start: 0.9211 (m) cc_final: 0.8393 (t) REVERT: H 179 MET cc_start: 0.8427 (ppp) cc_final: 0.8032 (ppp) REVERT: H 184 ASP cc_start: 0.8043 (p0) cc_final: 0.7671 (p0) REVERT: H 252 THR cc_start: 0.9071 (p) cc_final: 0.8793 (p) REVERT: H 265 GLN cc_start: 0.8840 (tt0) cc_final: 0.8236 (mt0) REVERT: H 412 ARG cc_start: 0.7942 (ptt-90) cc_final: 0.7537 (ptt180) outliers start: 93 outliers final: 47 residues processed: 609 average time/residue: 0.1847 time to fit residues: 183.5348 Evaluate side-chains 549 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 490 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 438 LYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 495 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [342, 0, 155, 99, 243, 226, 192, 195, 307, 107, 303] chunk 342 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 307 optimal weight: 0.0670 chunk 107 optimal weight: 1.9990 chunk 303 optimal weight: 0.9980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 507 HIS ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.151392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.120136 restraints weight = 38502.333| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.31 r_work: 0.3210 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31534 Z= 0.142 Angle : 0.606 8.082 42756 Z= 0.296 Chirality : 0.046 0.167 4868 Planarity : 0.003 0.035 5360 Dihedral : 15.660 179.039 4582 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.50 % Allowed : 13.49 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.13), residues: 3916 helix: -0.02 (0.14), residues: 1356 sheet: -1.03 (0.25), residues: 428 loop : -1.24 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 512 TYR 0.015 0.001 TYR H 509 PHE 0.023 0.001 PHE F 99 HIS 0.007 0.001 HIS F 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (31528) covalent geometry : angle 0.60648 / 0.30 (42756) hydrogen bonds : bond 0.02914 / 1.93 ( 1025) hydrogen bonds : angle 4.87982 / 3.42 ( 2913) Misc. bond : bond 0.00189 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 543 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8197 (t0) REVERT: A 126 ARG cc_start: 0.6595 (mtt90) cc_final: 0.5137 (mtp180) REVERT: A 150 MET cc_start: 0.7368 (mmm) cc_final: 0.6798 (tpt) REVERT: A 170 GLU cc_start: 0.5856 (OUTLIER) cc_final: 0.5074 (mt-10) REVERT: A 179 MET cc_start: 0.8250 (pp-130) cc_final: 0.7176 (pp-130) REVERT: A 192 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7711 (tp) REVERT: A 410 LYS cc_start: 0.7545 (mtpp) cc_final: 0.7246 (mmtt) REVERT: A 438 LYS cc_start: 0.7733 (ptmt) cc_final: 0.6502 (tptm) REVERT: E 36 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8243 (pp) REVERT: E 94 ASN cc_start: 0.9338 (t0) cc_final: 0.8870 (t0) REVERT: E 109 LYS cc_start: 0.8154 (mtmp) cc_final: 0.7866 (mttt) REVERT: E 124 LYS cc_start: 0.7619 (tppt) cc_final: 0.7384 (pptt) REVERT: E 149 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7153 (mtp85) REVERT: E 179 MET cc_start: 0.8470 (ppp) cc_final: 0.8016 (ppp) REVERT: E 184 ASP cc_start: 0.8055 (p0) cc_final: 0.7582 (p0) REVERT: E 224 ARG cc_start: 0.8395 (ttt90) cc_final: 0.8177 (ttt-90) REVERT: E 265 GLN cc_start: 0.8836 (tt0) cc_final: 0.8507 (mt0) REVERT: E 330 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9223 (pp) REVERT: E 352 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8924 (tm-30) REVERT: E 368 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7650 (mp-120) REVERT: E 412 ARG cc_start: 0.8068 (ptt-90) cc_final: 0.7675 (ptt180) REVERT: E 420 MET cc_start: 0.5682 (mpp) cc_final: 0.5338 (mpp) REVERT: E 438 LYS cc_start: 0.7655 (mtmm) cc_final: 0.7023 (mttp) REVERT: B 28 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7988 (t0) REVERT: B 150 MET cc_start: 0.7533 (mmm) cc_final: 0.7031 (tpt) REVERT: B 199 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7218 (pt0) REVERT: B 206 LYS cc_start: 0.7990 (tppt) cc_final: 0.7548 (mmmm) REVERT: B 274 ASP cc_start: 0.9049 (t70) cc_final: 0.8806 (t0) REVERT: B 410 LYS cc_start: 0.7739 (ttmm) cc_final: 0.7031 (mmtt) REVERT: F 94 ASN cc_start: 0.9381 (t160) cc_final: 0.9144 (t0) REVERT: F 109 LYS cc_start: 0.8310 (mttt) cc_final: 0.7820 (mttt) REVERT: F 179 MET cc_start: 0.8452 (ppp) cc_final: 0.8179 (ppp) REVERT: F 184 ASP cc_start: 0.8167 (p0) cc_final: 0.7684 (p0) REVERT: F 254 GLU cc_start: 0.8290 (mp0) cc_final: 0.8049 (mp0) REVERT: F 265 GLN cc_start: 0.8885 (tt0) cc_final: 0.8363 (mt0) REVERT: F 352 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8731 (tm-30) REVERT: F 412 ARG cc_start: 0.7913 (ptt-90) cc_final: 0.7378 (ptt180) REVERT: C 179 MET cc_start: 0.8126 (pp-130) cc_final: 0.7232 (pp-130) REVERT: C 192 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7699 (tp) REVERT: C 206 LYS cc_start: 0.7703 (mmmm) cc_final: 0.7243 (mmmm) REVERT: C 404 ASP cc_start: 0.6075 (t0) cc_final: 0.5794 (t0) REVERT: C 410 LYS cc_start: 0.7444 (mtpp) cc_final: 0.6884 (mmtt) REVERT: G 36 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8243 (pp) REVERT: G 94 ASN cc_start: 0.9337 (t160) cc_final: 0.9075 (t0) REVERT: G 179 MET cc_start: 0.8439 (ppp) cc_final: 0.7895 (ppp) REVERT: G 265 GLN cc_start: 0.8858 (tt0) cc_final: 0.8464 (mt0) REVERT: G 330 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.8988 (pp) REVERT: G 352 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8910 (tm-30) REVERT: D 28 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8015 (t0) REVERT: D 103 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: D 126 ARG cc_start: 0.6892 (mtt-85) cc_final: 0.4609 (mtt-85) REVERT: D 179 MET cc_start: 0.8438 (pp-130) cc_final: 0.7461 (pp-130) REVERT: D 192 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7456 (tp) REVERT: D 206 LYS cc_start: 0.8057 (tppt) cc_final: 0.7564 (mmmm) REVERT: D 274 ASP cc_start: 0.9076 (t70) cc_final: 0.8845 (t0) REVERT: H 36 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8192 (pp) REVERT: H 94 ASN cc_start: 0.9329 (t160) cc_final: 0.9115 (t0) REVERT: H 159 SER cc_start: 0.9269 (m) cc_final: 0.8426 (t) REVERT: H 179 MET cc_start: 0.8426 (ppp) cc_final: 0.7457 (ppp) REVERT: H 184 ASP cc_start: 0.8121 (p0) cc_final: 0.7742 (p0) REVERT: H 252 THR cc_start: 0.9080 (p) cc_final: 0.8800 (p) REVERT: H 265 GLN cc_start: 0.8861 (tt0) cc_final: 0.8251 (mt0) REVERT: H 412 ARG cc_start: 0.8037 (ptt-90) cc_final: 0.7690 (ptt180) outliers start: 113 outliers final: 64 residues processed: 610 average time/residue: 0.1918 time to fit residues: 190.1464 Evaluate side-chains 574 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 496 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 334 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 495 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [16, 73, 153, 272, 142, 24, 372, 13, 163, 260, 266] chunk 16 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 272 optimal weight: 0.0970 chunk 142 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 372 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 163 optimal weight: 0.0670 chunk 260 optimal weight: 0.5980 chunk 266 optimal weight: 6.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN E 466 HIS ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 507 HIS ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN G 368 GLN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN H 112 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.154093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122974 restraints weight = 38283.897| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.29 r_work: 0.3247 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31534 Z= 0.107 Angle : 0.579 7.690 42756 Z= 0.280 Chirality : 0.044 0.189 4868 Planarity : 0.003 0.035 5360 Dihedral : 15.149 174.907 4582 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.26 % Allowed : 15.48 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.13), residues: 3916 helix: 0.34 (0.15), residues: 1360 sheet: -0.99 (0.23), residues: 488 loop : -1.11 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 224 TYR 0.013 0.001 TYR H 509 PHE 0.014 0.001 PHE B 165 HIS 0.007 0.000 HIS F 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (31528) covalent geometry : angle 0.57865 / 0.28 (42756) hydrogen bonds : bond 0.02642 / 1.76 ( 1025) hydrogen bonds : angle 4.74075 / 3.34 ( 2913) Misc. bond : bond 0.00194 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 539 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8184 (t0) REVERT: A 80 ILE cc_start: 0.8912 (pp) cc_final: 0.8701 (mt) REVERT: A 126 ARG cc_start: 0.6552 (mtt90) cc_final: 0.5203 (mtp180) REVERT: A 150 MET cc_start: 0.7344 (mmm) cc_final: 0.6663 (tpt) REVERT: A 170 GLU cc_start: 0.5851 (OUTLIER) cc_final: 0.5154 (mt-10) REVERT: A 179 MET cc_start: 0.8275 (pp-130) cc_final: 0.7174 (pp-130) REVERT: A 192 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7678 (tp) REVERT: A 410 LYS cc_start: 0.7533 (mtpp) cc_final: 0.7081 (mmtt) REVERT: A 438 LYS cc_start: 0.7744 (ptmt) cc_final: 0.6464 (tptm) REVERT: E 36 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7888 (pp) REVERT: E 94 ASN cc_start: 0.9337 (t0) cc_final: 0.9009 (t0) REVERT: E 109 LYS cc_start: 0.8020 (mtmp) cc_final: 0.7741 (mttt) REVERT: E 149 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.7066 (mtp85) REVERT: E 179 MET cc_start: 0.8366 (ppp) cc_final: 0.7914 (ppp) REVERT: E 184 ASP cc_start: 0.8043 (p0) cc_final: 0.7574 (p0) REVERT: E 265 GLN cc_start: 0.8754 (tt0) cc_final: 0.8494 (mt0) REVERT: E 330 ILE cc_start: 0.9469 (OUTLIER) cc_final: 0.9232 (pp) REVERT: E 352 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8887 (tm-30) REVERT: E 412 ARG cc_start: 0.8057 (ptt-90) cc_final: 0.7459 (ptt180) REVERT: E 438 LYS cc_start: 0.7667 (mtmm) cc_final: 0.7069 (mttp) REVERT: B 28 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7975 (t0) REVERT: B 150 MET cc_start: 0.7379 (mmm) cc_final: 0.6885 (tpt) REVERT: B 199 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7147 (pt0) REVERT: B 274 ASP cc_start: 0.9067 (t70) cc_final: 0.8860 (t0) REVERT: B 410 LYS cc_start: 0.7707 (ttmm) cc_final: 0.7023 (mmtt) REVERT: F 94 ASN cc_start: 0.9352 (t160) cc_final: 0.9110 (t0) REVERT: F 109 LYS cc_start: 0.8274 (mttt) cc_final: 0.7812 (mttt) REVERT: F 179 MET cc_start: 0.8471 (ppp) cc_final: 0.8218 (ppp) REVERT: F 184 ASP cc_start: 0.8186 (p0) cc_final: 0.7718 (p0) REVERT: F 265 GLN cc_start: 0.8830 (tt0) cc_final: 0.8333 (mt0) REVERT: F 352 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8364 (tm-30) REVERT: F 412 ARG cc_start: 0.7917 (ptt-90) cc_final: 0.7440 (ptt180) REVERT: C 28 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.8045 (t0) REVERT: C 80 ILE cc_start: 0.8981 (pp) cc_final: 0.8755 (mt) REVERT: C 150 MET cc_start: 0.6881 (mmm) cc_final: 0.6322 (tpt) REVERT: C 179 MET cc_start: 0.8110 (pp-130) cc_final: 0.7177 (pp-130) REVERT: C 183 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: C 192 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7526 (tp) REVERT: C 206 LYS cc_start: 0.7624 (mmmm) cc_final: 0.7276 (mmmm) REVERT: C 404 ASP cc_start: 0.6003 (t0) cc_final: 0.5767 (t0) REVERT: C 410 LYS cc_start: 0.7456 (mtpp) cc_final: 0.6948 (mmtt) REVERT: G 36 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8028 (pp) REVERT: G 94 ASN cc_start: 0.9342 (t160) cc_final: 0.9085 (t0) REVERT: G 179 MET cc_start: 0.8467 (ppp) cc_final: 0.7913 (ppp) REVERT: G 265 GLN cc_start: 0.8836 (tt0) cc_final: 0.8499 (mt0) REVERT: G 330 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9037 (pp) REVERT: D 28 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8023 (t0) REVERT: D 103 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: D 126 ARG cc_start: 0.6830 (mtt-85) cc_final: 0.4626 (mtt-85) REVERT: D 150 MET cc_start: 0.7430 (mmm) cc_final: 0.6859 (tpt) REVERT: D 179 MET cc_start: 0.8402 (pp-130) cc_final: 0.7113 (pp-130) REVERT: D 192 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7437 (tp) REVERT: D 206 LYS cc_start: 0.8047 (tppt) cc_final: 0.7602 (mmmm) REVERT: D 274 ASP cc_start: 0.9121 (t70) cc_final: 0.8917 (t0) REVERT: H 36 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8121 (pp) REVERT: H 94 ASN cc_start: 0.9359 (t0) cc_final: 0.9113 (t0) REVERT: H 159 SER cc_start: 0.9221 (m) cc_final: 0.8306 (t) REVERT: H 179 MET cc_start: 0.8237 (ppp) cc_final: 0.7326 (ppp) REVERT: H 184 ASP cc_start: 0.8113 (p0) cc_final: 0.7737 (p0) REVERT: H 252 THR cc_start: 0.9001 (p) cc_final: 0.8712 (p) REVERT: H 265 GLN cc_start: 0.8840 (tt0) cc_final: 0.8263 (mt0) REVERT: H 385 MET cc_start: 0.8752 (ttp) cc_final: 0.8547 (ttm) REVERT: H 412 ARG cc_start: 0.8034 (ptt-90) cc_final: 0.7665 (ptt180) outliers start: 105 outliers final: 61 residues processed: 599 average time/residue: 0.1850 time to fit residues: 180.8321 Evaluate side-chains 572 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 496 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 368 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 370 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [106, 104, 101, 57, 271, 96, 210, 246, 183, 374, 370] chunk 106 optimal weight: 0.5980 chunk 104 optimal weight: 0.0870 chunk 101 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 271 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 374 optimal weight: 2.9990 chunk 370 optimal weight: 0.1980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN B 343 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.149986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.120279 restraints weight = 37904.085| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.18 r_work: 0.3219 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31534 Z= 0.107 Angle : 0.581 8.088 42756 Z= 0.281 Chirality : 0.044 0.265 4868 Planarity : 0.003 0.035 5360 Dihedral : 14.870 179.023 4582 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.13 % Allowed : 16.35 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.14), residues: 3916 helix: 0.57 (0.15), residues: 1360 sheet: -0.86 (0.23), residues: 492 loop : -1.04 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 224 TYR 0.012 0.001 TYR H 509 PHE 0.027 0.001 PHE F 139 HIS 0.004 0.000 HIS F 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (31528) covalent geometry : angle 0.58147 / 0.28 (42756) hydrogen bonds : bond 0.02577 / 1.71 ( 1025) hydrogen bonds : angle 4.67338 / 3.29 ( 2913) Misc. bond : bond 0.00140 / 0.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 524 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8204 (t0) REVERT: A 150 MET cc_start: 0.7224 (mmm) cc_final: 0.6945 (tpt) REVERT: A 170 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.5203 (mt-10) REVERT: A 179 MET cc_start: 0.8136 (pp-130) cc_final: 0.7022 (pp-130) REVERT: A 192 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7577 (tp) REVERT: A 410 LYS cc_start: 0.7435 (mtpp) cc_final: 0.6979 (mmtt) REVERT: A 438 LYS cc_start: 0.7735 (ptmt) cc_final: 0.6338 (tptm) REVERT: E 36 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8123 (pp) REVERT: E 94 ASN cc_start: 0.9362 (t0) cc_final: 0.9035 (t0) REVERT: E 109 LYS cc_start: 0.7942 (mtmp) cc_final: 0.7630 (mttt) REVERT: E 149 ARG cc_start: 0.7519 (mtm-85) cc_final: 0.6911 (mtp85) REVERT: E 184 ASP cc_start: 0.8083 (p0) cc_final: 0.7640 (p0) REVERT: E 265 GLN cc_start: 0.8684 (tt0) cc_final: 0.8399 (mt0) REVERT: E 330 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9201 (pp) REVERT: E 352 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8799 (tm-30) REVERT: E 412 ARG cc_start: 0.7804 (ptt-90) cc_final: 0.7260 (ptt180) REVERT: E 438 LYS cc_start: 0.7559 (mtmm) cc_final: 0.6945 (mttp) REVERT: B 28 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8015 (t0) REVERT: B 150 MET cc_start: 0.7330 (mmm) cc_final: 0.6782 (tpt) REVERT: B 274 ASP cc_start: 0.9058 (t70) cc_final: 0.8852 (t0) REVERT: B 343 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6706 (tt0) REVERT: B 410 LYS cc_start: 0.7588 (ttmm) cc_final: 0.6867 (mmtt) REVERT: F 94 ASN cc_start: 0.9373 (OUTLIER) cc_final: 0.9139 (t0) REVERT: F 109 LYS cc_start: 0.8117 (mttt) cc_final: 0.7724 (mttt) REVERT: F 179 MET cc_start: 0.8442 (ppp) cc_final: 0.8137 (ppp) REVERT: F 184 ASP cc_start: 0.8232 (p0) cc_final: 0.7788 (p0) REVERT: F 265 GLN cc_start: 0.8792 (tt0) cc_final: 0.8250 (mt0) REVERT: F 352 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8657 (tp30) REVERT: F 412 ARG cc_start: 0.7707 (ptt-90) cc_final: 0.7187 (ptt180) REVERT: C 28 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8052 (t0) REVERT: C 150 MET cc_start: 0.6655 (mmm) cc_final: 0.6131 (tpt) REVERT: C 183 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: C 192 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7553 (tp) REVERT: C 388 SER cc_start: 0.8938 (p) cc_final: 0.8736 (p) REVERT: C 410 LYS cc_start: 0.7361 (mtpp) cc_final: 0.6863 (mmtt) REVERT: G 36 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8054 (pp) REVERT: G 94 ASN cc_start: 0.9370 (OUTLIER) cc_final: 0.9109 (t0) REVERT: G 179 MET cc_start: 0.8287 (ppp) cc_final: 0.7099 (ppp) REVERT: G 265 GLN cc_start: 0.8718 (tt0) cc_final: 0.8324 (mt0) REVERT: G 327 SER cc_start: 0.8556 (p) cc_final: 0.8109 (t) REVERT: G 330 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.8932 (pp) REVERT: D 28 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8092 (t0) REVERT: D 103 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: D 126 ARG cc_start: 0.6629 (mtt-85) cc_final: 0.4441 (mtt-85) REVERT: D 150 MET cc_start: 0.7253 (mmm) cc_final: 0.6693 (tpt) REVERT: D 179 MET cc_start: 0.8341 (pp-130) cc_final: 0.7033 (pp-130) REVERT: D 192 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7451 (tp) REVERT: H 36 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8090 (pp) REVERT: H 94 ASN cc_start: 0.9398 (t0) cc_final: 0.9146 (t0) REVERT: H 159 SER cc_start: 0.9180 (m) cc_final: 0.8191 (t) REVERT: H 179 MET cc_start: 0.8170 (ppp) cc_final: 0.7254 (ppp) REVERT: H 184 ASP cc_start: 0.8187 (p0) cc_final: 0.7853 (p0) REVERT: H 228 LYS cc_start: 0.8274 (ttmt) cc_final: 0.8063 (ttmm) REVERT: H 252 THR cc_start: 0.8995 (p) cc_final: 0.8700 (p) REVERT: H 265 GLN cc_start: 0.8775 (tt0) cc_final: 0.8161 (mt0) REVERT: H 330 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8826 (pp) REVERT: H 385 MET cc_start: 0.8709 (ttp) cc_final: 0.8449 (ttm) REVERT: H 412 ARG cc_start: 0.7839 (ptt-90) cc_final: 0.7460 (ptt180) outliers start: 101 outliers final: 65 residues processed: 588 average time/residue: 0.1876 time to fit residues: 180.2008 Evaluate side-chains 577 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 493 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 438 LYS Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 495 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [374, 309, 162, 106, 236, 83, 190, 184, 160, 250, 229] chunk 374 optimal weight: 0.0970 chunk 309 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 236 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 250 optimal weight: 4.9990 chunk 229 optimal weight: 0.0010 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN B 343 GLN F 94 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 368 GLN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.148525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.117281 restraints weight = 38100.790| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.31 r_work: 0.3135 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31534 Z= 0.154 Angle : 0.611 8.547 42756 Z= 0.297 Chirality : 0.046 0.247 4868 Planarity : 0.003 0.034 5360 Dihedral : 14.546 176.176 4582 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.26 % Allowed : 16.59 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3916 helix: 0.58 (0.15), residues: 1364 sheet: -0.85 (0.24), residues: 448 loop : -0.98 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 224 TYR 0.019 0.001 TYR H 509 PHE 0.019 0.001 PHE F 139 HIS 0.004 0.001 HIS F 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.15 (31528) covalent geometry : angle 0.61119 / 0.30 (42756) hydrogen bonds : bond 0.02837 / 1.88 ( 1025) hydrogen bonds : angle 4.73122 / 3.32 ( 2913) Misc. bond : bond 0.00169 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 513 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8207 (t0) REVERT: A 80 ILE cc_start: 0.8780 (pp) cc_final: 0.8558 (mt) REVERT: A 150 MET cc_start: 0.7207 (mmm) cc_final: 0.6898 (tpt) REVERT: A 170 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.5143 (mt-10) REVERT: A 179 MET cc_start: 0.8218 (pp-130) cc_final: 0.7100 (pp-130) REVERT: A 192 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7722 (tp) REVERT: A 410 LYS cc_start: 0.7445 (mtpp) cc_final: 0.6981 (mmtt) REVERT: A 412 ARG cc_start: 0.8056 (ptt-90) cc_final: 0.7778 (ptt-90) REVERT: A 438 LYS cc_start: 0.7740 (ptmt) cc_final: 0.6340 (tptm) REVERT: E 36 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8243 (pp) REVERT: E 94 ASN cc_start: 0.9376 (t0) cc_final: 0.9047 (t0) REVERT: E 109 LYS cc_start: 0.8140 (mtmp) cc_final: 0.7822 (mttt) REVERT: E 149 ARG cc_start: 0.7533 (mtm-85) cc_final: 0.6926 (mtp85) REVERT: E 179 MET cc_start: 0.8306 (ppp) cc_final: 0.7566 (ppp) REVERT: E 184 ASP cc_start: 0.8101 (p0) cc_final: 0.7639 (p0) REVERT: E 235 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8275 (pp) REVERT: E 265 GLN cc_start: 0.8779 (tt0) cc_final: 0.8489 (mt0) REVERT: E 330 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9222 (pp) REVERT: E 352 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8889 (tm-30) REVERT: E 412 ARG cc_start: 0.7958 (ptt-90) cc_final: 0.7553 (ptt180) REVERT: E 438 LYS cc_start: 0.7567 (mtmm) cc_final: 0.6968 (mttp) REVERT: B 28 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8006 (t0) REVERT: B 150 MET cc_start: 0.7344 (mmm) cc_final: 0.6709 (tpt) REVERT: B 274 ASP cc_start: 0.9060 (t70) cc_final: 0.8818 (t0) REVERT: F 94 ASN cc_start: 0.9417 (t0) cc_final: 0.9179 (t0) REVERT: F 109 LYS cc_start: 0.8203 (mttt) cc_final: 0.7711 (mttt) REVERT: F 128 ARG cc_start: 0.7713 (mtm110) cc_final: 0.7344 (mmt90) REVERT: F 179 MET cc_start: 0.8453 (ppp) cc_final: 0.8171 (ppp) REVERT: F 184 ASP cc_start: 0.8226 (p0) cc_final: 0.7793 (p0) REVERT: F 265 GLN cc_start: 0.8869 (tt0) cc_final: 0.8339 (mt0) REVERT: F 330 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8962 (pp) REVERT: F 352 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8668 (tm-30) REVERT: F 412 ARG cc_start: 0.7827 (ptt-90) cc_final: 0.7333 (ptt180) REVERT: C 28 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8178 (t0) REVERT: C 80 ILE cc_start: 0.8811 (pp) cc_final: 0.8585 (mt) REVERT: C 150 MET cc_start: 0.6694 (mmm) cc_final: 0.6213 (tpt) REVERT: C 410 LYS cc_start: 0.7368 (mtpp) cc_final: 0.6839 (mmtt) REVERT: C 412 ARG cc_start: 0.8066 (ptt-90) cc_final: 0.7739 (ptt-90) REVERT: G 36 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8183 (pp) REVERT: G 94 ASN cc_start: 0.9408 (t0) cc_final: 0.9147 (t0) REVERT: G 265 GLN cc_start: 0.8801 (tt0) cc_final: 0.8418 (mt0) REVERT: G 327 SER cc_start: 0.8672 (p) cc_final: 0.8247 (t) REVERT: G 330 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.8990 (pp) REVERT: G 412 ARG cc_start: 0.7536 (ptt-90) cc_final: 0.7044 (ptt180) REVERT: D 16 ASP cc_start: 0.8539 (t70) cc_final: 0.8339 (t70) REVERT: D 28 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7983 (t0) REVERT: D 103 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: D 126 ARG cc_start: 0.6677 (mtt-85) cc_final: 0.4479 (mtt-85) REVERT: D 150 MET cc_start: 0.7126 (mmm) cc_final: 0.6681 (tpt) REVERT: D 179 MET cc_start: 0.8403 (pp-130) cc_final: 0.7100 (pp-130) REVERT: D 512 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.5469 (tmt-80) REVERT: H 36 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8401 (pp) REVERT: H 94 ASN cc_start: 0.9411 (t0) cc_final: 0.9133 (t0) REVERT: H 159 SER cc_start: 0.9189 (m) cc_final: 0.8241 (t) REVERT: H 179 MET cc_start: 0.8107 (ppp) cc_final: 0.7190 (ppp) REVERT: H 184 ASP cc_start: 0.8206 (p0) cc_final: 0.7853 (p0) REVERT: H 252 THR cc_start: 0.9132 (p) cc_final: 0.8858 (p) REVERT: H 265 GLN cc_start: 0.8843 (tt0) cc_final: 0.8258 (mt0) REVERT: H 330 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8930 (pp) REVERT: H 385 MET cc_start: 0.8870 (ttp) cc_final: 0.8552 (ttm) REVERT: H 412 ARG cc_start: 0.7935 (ptt-90) cc_final: 0.7419 (ptt180) outliers start: 105 outliers final: 69 residues processed: 581 average time/residue: 0.1838 time to fit residues: 174.6392 Evaluate side-chains 572 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 487 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 438 LYS Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 368 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 512 ARG Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 495 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [269, 167, 65, 367, 158, 384, 316, 108, 212, 242, 241] chunk 269 optimal weight: 0.9990 chunk 167 optimal weight: 0.7980 chunk 65 optimal weight: 0.0060 chunk 367 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 384 optimal weight: 5.9990 chunk 316 optimal weight: 0.5980 chunk 108 optimal weight: 0.1980 chunk 212 optimal weight: 0.0870 chunk 242 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN B 343 GLN F 33 ASN F 94 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS G 94 ASN G 368 GLN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.155734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124760 restraints weight = 38333.555| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.31 r_work: 0.3266 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31534 Z= 0.096 Angle : 0.571 8.615 42756 Z= 0.276 Chirality : 0.044 0.213 4868 Planarity : 0.003 0.036 5360 Dihedral : 13.823 172.135 4578 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.82 % Allowed : 17.46 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3916 helix: 0.84 (0.15), residues: 1364 sheet: -0.50 (0.24), residues: 456 loop : -0.94 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 224 TYR 0.018 0.001 TYR H 509 PHE 0.025 0.001 PHE E 139 HIS 0.003 0.000 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (31528) covalent geometry : angle 0.57120 / 0.28 (42756) hydrogen bonds : bond 0.02405 / 1.59 ( 1025) hydrogen bonds : angle 4.59081 / 3.24 ( 2913) Misc. bond : bond 0.00123 / 0.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 526 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8165 (t0) REVERT: A 78 MET cc_start: 0.9232 (tpp) cc_final: 0.8930 (tpp) REVERT: A 80 ILE cc_start: 0.8910 (pp) cc_final: 0.8687 (mt) REVERT: A 150 MET cc_start: 0.7042 (mmm) cc_final: 0.6707 (tpt) REVERT: A 170 GLU cc_start: 0.5865 (OUTLIER) cc_final: 0.5049 (mt-10) REVERT: A 179 MET cc_start: 0.8259 (pp-130) cc_final: 0.7209 (pp-130) REVERT: A 192 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7519 (tp) REVERT: A 216 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.7070 (t0) REVERT: A 410 LYS cc_start: 0.7487 (mtpp) cc_final: 0.7150 (mmtt) REVERT: A 412 ARG cc_start: 0.8046 (ptt-90) cc_final: 0.7763 (ptt-90) REVERT: A 438 LYS cc_start: 0.7761 (ptmt) cc_final: 0.6472 (tptm) REVERT: A 487 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8616 (tt0) REVERT: E 36 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8010 (pp) REVERT: E 94 ASN cc_start: 0.9337 (t0) cc_final: 0.8993 (t0) REVERT: E 149 ARG cc_start: 0.7534 (mtm-85) cc_final: 0.6946 (mtp85) REVERT: E 179 MET cc_start: 0.8227 (ppp) cc_final: 0.7641 (ppp) REVERT: E 184 ASP cc_start: 0.7992 (p0) cc_final: 0.7560 (p0) REVERT: E 224 ARG cc_start: 0.8353 (ttt90) cc_final: 0.7971 (ttt-90) REVERT: E 235 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8204 (pp) REVERT: E 265 GLN cc_start: 0.8698 (tt0) cc_final: 0.8485 (mt0) REVERT: E 330 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9264 (pp) REVERT: E 352 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8900 (tm-30) REVERT: E 412 ARG cc_start: 0.8095 (ptt-90) cc_final: 0.7562 (ptt180) REVERT: E 438 LYS cc_start: 0.7612 (mtmm) cc_final: 0.7054 (mttp) REVERT: B 150 MET cc_start: 0.7311 (mmm) cc_final: 0.6579 (tpt) REVERT: B 334 GLN cc_start: 0.8202 (mt0) cc_final: 0.7942 (mt0) REVERT: B 343 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: B 410 LYS cc_start: 0.7693 (ttmm) cc_final: 0.6969 (mmtt) REVERT: B 412 ARG cc_start: 0.7921 (ptt-90) cc_final: 0.7641 (ptt-90) REVERT: B 487 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8626 (tt0) REVERT: F 94 ASN cc_start: 0.9391 (OUTLIER) cc_final: 0.8935 (t0) REVERT: F 109 LYS cc_start: 0.8136 (mttt) cc_final: 0.7658 (mttt) REVERT: F 128 ARG cc_start: 0.7715 (mtm110) cc_final: 0.7365 (mmt90) REVERT: F 179 MET cc_start: 0.8450 (ppp) cc_final: 0.8200 (ppp) REVERT: F 184 ASP cc_start: 0.8179 (p0) cc_final: 0.7737 (p0) REVERT: F 265 GLN cc_start: 0.8794 (tt0) cc_final: 0.8336 (mt0) REVERT: F 330 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9061 (pp) REVERT: F 352 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8390 (tm-30) REVERT: F 412 ARG cc_start: 0.7888 (ptt-90) cc_final: 0.7392 (ptt180) REVERT: C 150 MET cc_start: 0.6718 (mmm) cc_final: 0.6294 (tpt) REVERT: C 410 LYS cc_start: 0.7431 (mtpp) cc_final: 0.6942 (mmtt) REVERT: C 412 ARG cc_start: 0.8057 (ptt-90) cc_final: 0.7637 (ptt-90) REVERT: G 36 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7860 (pp) REVERT: G 94 ASN cc_start: 0.9384 (t160) cc_final: 0.9083 (t0) REVERT: G 179 MET cc_start: 0.8391 (ppp) cc_final: 0.7656 (ppp) REVERT: G 265 GLN cc_start: 0.8754 (tt0) cc_final: 0.8479 (mt0) REVERT: G 327 SER cc_start: 0.8675 (p) cc_final: 0.8300 (t) REVERT: G 330 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9035 (pp) REVERT: D 16 ASP cc_start: 0.8523 (t70) cc_final: 0.8310 (t70) REVERT: D 28 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.8018 (t0) REVERT: D 78 MET cc_start: 0.9176 (tpp) cc_final: 0.8890 (tpp) REVERT: D 80 ILE cc_start: 0.9083 (pp) cc_final: 0.8779 (mt) REVERT: D 103 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: D 126 ARG cc_start: 0.6756 (mtt-85) cc_final: 0.4557 (mtt-85) REVERT: D 150 MET cc_start: 0.7094 (mmm) cc_final: 0.6531 (tpt) REVERT: D 179 MET cc_start: 0.8412 (pp-130) cc_final: 0.7140 (pp-130) REVERT: D 410 LYS cc_start: 0.7645 (ttmm) cc_final: 0.7416 (tppt) REVERT: D 512 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.5408 (tmt-80) REVERT: H 36 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8138 (pp) REVERT: H 94 ASN cc_start: 0.9380 (t0) cc_final: 0.9093 (t0) REVERT: H 159 SER cc_start: 0.9095 (m) cc_final: 0.8242 (t) REVERT: H 184 ASP cc_start: 0.8135 (p0) cc_final: 0.7784 (p0) REVERT: H 252 THR cc_start: 0.8941 (p) cc_final: 0.8649 (p) REVERT: H 265 GLN cc_start: 0.8798 (tt0) cc_final: 0.8295 (mt0) REVERT: H 330 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8943 (pp) REVERT: H 385 MET cc_start: 0.8787 (ttp) cc_final: 0.8531 (ttm) REVERT: H 412 ARG cc_start: 0.8021 (ptt-90) cc_final: 0.7520 (ptt180) outliers start: 91 outliers final: 60 residues processed: 588 average time/residue: 0.1851 time to fit residues: 178.8307 Evaluate side-chains 555 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 478 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 438 LYS Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 368 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 512 ARG Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 495 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [268, 339, 67, 353, 355, 12, 236, 111, 209, 316, 173] chunk 268 optimal weight: 2.9990 chunk 339 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 353 optimal weight: 3.9990 chunk 355 optimal weight: 0.0030 chunk 12 optimal weight: 0.0270 chunk 236 optimal weight: 0.3980 chunk 111 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 chunk 316 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 overall best weight: 0.4650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 202 GLN B 343 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN H 334 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.154790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123838 restraints weight = 38101.686| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.30 r_work: 0.3218 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31534 Z= 0.107 Angle : 0.596 9.500 42756 Z= 0.287 Chirality : 0.044 0.295 4868 Planarity : 0.003 0.035 5360 Dihedral : 13.534 170.929 4578 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.67 % Allowed : 18.11 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.14), residues: 3916 helix: 0.93 (0.15), residues: 1364 sheet: -0.81 (0.25), residues: 424 loop : -0.88 (0.14), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 224 TYR 0.018 0.001 TYR H 509 PHE 0.021 0.001 PHE E 139 HIS 0.003 0.000 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (31528) covalent geometry : angle 0.59552 / 0.29 (42756) hydrogen bonds : bond 0.02438 / 1.63 ( 1025) hydrogen bonds : angle 4.52025 / 3.19 ( 2913) Misc. bond : bond 0.00083 / 0.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 502 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.8005 (t0) REVERT: A 80 ILE cc_start: 0.8858 (pp) cc_final: 0.8624 (mt) REVERT: A 150 MET cc_start: 0.6924 (mmm) cc_final: 0.6592 (tpt) REVERT: A 170 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.5068 (mt-10) REVERT: A 179 MET cc_start: 0.8128 (pp-130) cc_final: 0.7091 (pp-130) REVERT: A 192 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7543 (tp) REVERT: A 216 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.7020 (t0) REVERT: A 410 LYS cc_start: 0.7443 (mtpp) cc_final: 0.7108 (mmtt) REVERT: A 412 ARG cc_start: 0.7951 (ptt-90) cc_final: 0.7687 (ptt-90) REVERT: A 438 LYS cc_start: 0.7741 (ptmt) cc_final: 0.6412 (tptm) REVERT: A 487 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8463 (tt0) REVERT: E 36 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8004 (pp) REVERT: E 94 ASN cc_start: 0.9329 (t0) cc_final: 0.8959 (t0) REVERT: E 149 ARG cc_start: 0.7419 (mtm-85) cc_final: 0.6858 (mtp85) REVERT: E 179 MET cc_start: 0.8193 (ppp) cc_final: 0.7556 (ppp) REVERT: E 184 ASP cc_start: 0.7964 (p0) cc_final: 0.7529 (p0) REVERT: E 224 ARG cc_start: 0.8159 (ttt90) cc_final: 0.7772 (ttt-90) REVERT: E 235 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8175 (pp) REVERT: E 330 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9205 (pp) REVERT: E 352 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8809 (tm-30) REVERT: E 412 ARG cc_start: 0.8043 (ptt-90) cc_final: 0.7521 (ptt180) REVERT: E 438 LYS cc_start: 0.7611 (mtmm) cc_final: 0.7086 (mttp) REVERT: B 28 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7847 (t0) REVERT: B 150 MET cc_start: 0.7122 (mmm) cc_final: 0.6798 (tpt) REVERT: B 334 GLN cc_start: 0.8087 (mt0) cc_final: 0.7794 (mt0) REVERT: B 410 LYS cc_start: 0.7627 (ttmm) cc_final: 0.6910 (mmtt) REVERT: B 412 ARG cc_start: 0.7881 (ptt-90) cc_final: 0.7472 (ptt-90) REVERT: F 94 ASN cc_start: 0.9404 (t0) cc_final: 0.9062 (t0) REVERT: F 109 LYS cc_start: 0.8050 (mttt) cc_final: 0.7548 (mttt) REVERT: F 128 ARG cc_start: 0.7598 (mtm110) cc_final: 0.7302 (mmt90) REVERT: F 179 MET cc_start: 0.8361 (ppp) cc_final: 0.8152 (ppp) REVERT: F 184 ASP cc_start: 0.8080 (p0) cc_final: 0.7639 (p0) REVERT: F 265 GLN cc_start: 0.8744 (tt0) cc_final: 0.8290 (mt0) REVERT: F 330 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8999 (pp) REVERT: F 352 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8187 (tm-30) REVERT: F 412 ARG cc_start: 0.7728 (ptt-90) cc_final: 0.7261 (ptt180) REVERT: C 71 ASP cc_start: 0.9031 (p0) cc_final: 0.8784 (p0) REVERT: C 150 MET cc_start: 0.6631 (mmm) cc_final: 0.6190 (tpt) REVERT: C 404 ASP cc_start: 0.5823 (t0) cc_final: 0.5276 (t0) REVERT: C 410 LYS cc_start: 0.7379 (mtpp) cc_final: 0.6888 (mmtt) REVERT: G 36 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7844 (pp) REVERT: G 82 MET cc_start: 0.9022 (tpp) cc_final: 0.8754 (mmm) REVERT: G 94 ASN cc_start: 0.9323 (OUTLIER) cc_final: 0.9028 (t0) REVERT: G 179 MET cc_start: 0.8375 (ppp) cc_final: 0.7615 (ppp) REVERT: G 184 ASP cc_start: 0.7947 (p0) cc_final: 0.7690 (t0) REVERT: G 265 GLN cc_start: 0.8663 (tt0) cc_final: 0.8422 (mt0) REVERT: G 327 SER cc_start: 0.8598 (p) cc_final: 0.8271 (t) REVERT: G 330 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8965 (pp) REVERT: D 28 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7882 (t0) REVERT: D 103 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: D 126 ARG cc_start: 0.6620 (mtt-85) cc_final: 0.4423 (mtt-85) REVERT: D 150 MET cc_start: 0.7039 (mmm) cc_final: 0.6459 (tpt) REVERT: D 179 MET cc_start: 0.8343 (pp-130) cc_final: 0.7042 (pp-130) REVERT: D 512 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.5401 (tmt-80) REVERT: H 36 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8086 (pp) REVERT: H 94 ASN cc_start: 0.9363 (t0) cc_final: 0.9041 (t0) REVERT: H 159 SER cc_start: 0.9114 (m) cc_final: 0.8177 (t) REVERT: H 179 MET cc_start: 0.8518 (ptm) cc_final: 0.7792 (ppp) REVERT: H 184 ASP cc_start: 0.8088 (p0) cc_final: 0.7730 (p0) REVERT: H 252 THR cc_start: 0.8878 (p) cc_final: 0.8587 (p) REVERT: H 265 GLN cc_start: 0.8729 (tt0) cc_final: 0.8241 (mt0) REVERT: H 330 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8863 (pp) REVERT: H 412 ARG cc_start: 0.7954 (ptt-90) cc_final: 0.7473 (ptt180) outliers start: 86 outliers final: 63 residues processed: 560 average time/residue: 0.1828 time to fit residues: 167.5777 Evaluate side-chains 559 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 479 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 438 LYS Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 512 ARG Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 495 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [168, 110, 51, 311, 286, 23, 48, 202, 88, 334, 92] chunk 168 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 311 optimal weight: 4.9990 chunk 286 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 0.0670 chunk 202 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 334 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 GLN B 202 GLN B 343 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN G 368 GLN D 198 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.154272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123214 restraints weight = 37962.080| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.29 r_work: 0.3248 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31534 Z= 0.115 Angle : 0.607 9.670 42756 Z= 0.292 Chirality : 0.044 0.255 4868 Planarity : 0.003 0.036 5360 Dihedral : 13.220 175.847 4578 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.67 % Allowed : 18.39 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3916 helix: 0.97 (0.15), residues: 1364 sheet: -0.90 (0.25), residues: 424 loop : -0.86 (0.14), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 224 TYR 0.018 0.001 TYR H 509 PHE 0.020 0.001 PHE E 139 HIS 0.003 0.000 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (31528) covalent geometry : angle 0.60658 / 0.29 (42756) hydrogen bonds : bond 0.02494 / 1.67 ( 1025) hydrogen bonds : angle 4.50580 / 3.18 ( 2913) Misc. bond : bond 0.00193 / 0.07 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 505 time to evaluate : 1.197 Fit side-chains REVERT: A 28 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8099 (t0) REVERT: A 80 ILE cc_start: 0.8958 (pp) cc_final: 0.8706 (mt) REVERT: A 150 MET cc_start: 0.6927 (mmm) cc_final: 0.6701 (tpt) REVERT: A 170 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5070 (mt-10) REVERT: A 179 MET cc_start: 0.8279 (pp-130) cc_final: 0.7243 (pp-130) REVERT: A 192 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7599 (tp) REVERT: A 216 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.7021 (t0) REVERT: A 410 LYS cc_start: 0.7508 (mtpp) cc_final: 0.7069 (mmtt) REVERT: A 412 ARG cc_start: 0.8034 (ptt-90) cc_final: 0.7777 (ptt-90) REVERT: A 438 LYS cc_start: 0.7800 (ptmt) cc_final: 0.6470 (tptm) REVERT: A 487 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8622 (tt0) REVERT: E 36 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8151 (pp) REVERT: E 94 ASN cc_start: 0.9386 (t0) cc_final: 0.9033 (t0) REVERT: E 149 ARG cc_start: 0.7431 (mtm-85) cc_final: 0.6881 (mtp85) REVERT: E 179 MET cc_start: 0.8295 (ppp) cc_final: 0.7614 (ppp) REVERT: E 184 ASP cc_start: 0.8011 (p0) cc_final: 0.7563 (p0) REVERT: E 224 ARG cc_start: 0.8405 (ttt90) cc_final: 0.8039 (ttt-90) REVERT: E 235 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8263 (pp) REVERT: E 330 ILE cc_start: 0.9476 (OUTLIER) cc_final: 0.9249 (pp) REVERT: E 352 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8919 (tm-30) REVERT: E 412 ARG cc_start: 0.8138 (ptt-90) cc_final: 0.7566 (ptt180) REVERT: E 438 LYS cc_start: 0.7637 (mtmm) cc_final: 0.7100 (mttp) REVERT: B 28 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7989 (t0) REVERT: B 71 ASP cc_start: 0.9144 (p0) cc_final: 0.8796 (p0) REVERT: B 150 MET cc_start: 0.7148 (mmm) cc_final: 0.6803 (tpt) REVERT: B 181 LYS cc_start: 0.7485 (mppt) cc_final: 0.7150 (mmmt) REVERT: B 334 GLN cc_start: 0.8215 (mt0) cc_final: 0.7958 (mt0) REVERT: B 412 ARG cc_start: 0.7886 (ptt-90) cc_final: 0.7624 (ptt-90) REVERT: F 94 ASN cc_start: 0.9422 (t0) cc_final: 0.8923 (t0) REVERT: F 128 ARG cc_start: 0.7675 (mtm110) cc_final: 0.7336 (mmt90) REVERT: F 179 MET cc_start: 0.8376 (ppp) cc_final: 0.8162 (ppp) REVERT: F 184 ASP cc_start: 0.8105 (p0) cc_final: 0.7703 (p0) REVERT: F 265 GLN cc_start: 0.8838 (tt0) cc_final: 0.8419 (mt0) REVERT: F 330 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9066 (pp) REVERT: F 352 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8362 (tm-30) REVERT: F 412 ARG cc_start: 0.7728 (ptt-90) cc_final: 0.7256 (ptt180) REVERT: C 150 MET cc_start: 0.6689 (mmm) cc_final: 0.6295 (tpt) REVERT: C 404 ASP cc_start: 0.5776 (t0) cc_final: 0.5404 (t70) REVERT: C 410 LYS cc_start: 0.7423 (mtpp) cc_final: 0.6908 (mmtt) REVERT: G 36 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8107 (pp) REVERT: G 82 MET cc_start: 0.9089 (tpp) cc_final: 0.8879 (mmt) REVERT: G 94 ASN cc_start: 0.9360 (OUTLIER) cc_final: 0.9068 (t0) REVERT: G 179 MET cc_start: 0.8174 (ppp) cc_final: 0.7700 (ppp) REVERT: G 265 GLN cc_start: 0.8767 (tt0) cc_final: 0.8492 (mt0) REVERT: G 327 SER cc_start: 0.8685 (p) cc_final: 0.8264 (t) REVERT: D 16 ASP cc_start: 0.8578 (t70) cc_final: 0.8234 (t0) REVERT: D 28 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.8034 (t0) REVERT: D 103 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: D 126 ARG cc_start: 0.6646 (mtt-85) cc_final: 0.4448 (mtt-85) REVERT: D 150 MET cc_start: 0.7061 (mmm) cc_final: 0.6458 (tpt) REVERT: D 179 MET cc_start: 0.8437 (pp-130) cc_final: 0.7158 (pp-130) REVERT: D 412 ARG cc_start: 0.8035 (ptt-90) cc_final: 0.7790 (ptt-90) REVERT: D 512 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.5401 (tmt-80) REVERT: H 36 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8280 (pp) REVERT: H 94 ASN cc_start: 0.9417 (t0) cc_final: 0.9077 (t0) REVERT: H 159 SER cc_start: 0.9111 (m) cc_final: 0.8186 (t) REVERT: H 179 MET cc_start: 0.8477 (ptm) cc_final: 0.7559 (ppp) REVERT: H 184 ASP cc_start: 0.8142 (p0) cc_final: 0.7782 (p0) REVERT: H 252 THR cc_start: 0.8966 (p) cc_final: 0.8683 (p) REVERT: H 265 GLN cc_start: 0.8822 (tt0) cc_final: 0.8306 (mt0) REVERT: H 330 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8968 (pp) REVERT: H 412 ARG cc_start: 0.8016 (ptt-90) cc_final: 0.7524 (ptt180) outliers start: 86 outliers final: 63 residues processed: 562 average time/residue: 0.1805 time to fit residues: 167.4083 Evaluate side-chains 557 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 478 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 438 LYS Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 368 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 512 ARG Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 495 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: [69, 374, 102, 257, 118, 327, 74, 340, 308, 372, 105] chunk 69 optimal weight: 0.0970 chunk 374 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 327 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 340 optimal weight: 5.9990 chunk 308 optimal weight: 7.9990 chunk 372 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 368 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.147652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.116038 restraints weight = 38302.495| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.32 r_work: 0.3116 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31534 Z= 0.177 Angle : 0.655 9.792 42756 Z= 0.319 Chirality : 0.047 0.277 4868 Planarity : 0.003 0.035 5360 Dihedral : 13.177 169.696 4578 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.54 % Allowed : 18.92 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3916 helix: 0.83 (0.15), residues: 1364 sheet: -0.88 (0.26), residues: 404 loop : -0.88 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 149 TYR 0.019 0.002 TYR H 509 PHE 0.033 0.002 PHE H 139 HIS 0.004 0.001 HIS F 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (31528) covalent geometry : angle 0.65526 / 0.32 (42756) hydrogen bonds : bond 0.02895 / 1.92 ( 1025) hydrogen bonds : angle 4.66265 / 3.28 ( 2913) Misc. bond : bond 0.00158 / 0.06 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7650.96 seconds wall clock time: 131 minutes 45.28 seconds (7905.28 seconds total)