Starting phenix.real_space_refine on Fri Mar 6 14:12:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6udo_20741/03_2026/6udo_20741.cif Found real_map, /net/cci-nas-00/data/ceres_data/6udo_20741/03_2026/6udo_20741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6udo_20741/03_2026/6udo_20741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6udo_20741/03_2026/6udo_20741.map" model { file = "/net/cci-nas-00/data/ceres_data/6udo_20741/03_2026/6udo_20741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6udo_20741/03_2026/6udo_20741.cif" } resolution = 3.21 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= 0.058 sd= 3.698 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 176 5.16 5 C 19544 2.51 5 N 5376 2.21 5 O 6216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31392 Number of models: 1 Model: "" Number of chains: 24 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: "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: "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: "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: "E" 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: 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: 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: 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: "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: "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: "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: "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: "M" 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: "N" 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: "O" 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: "P" 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: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 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: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 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: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 6.71, per 1000 atoms: 0.21 Number of scatterers: 31392 At special positions: 0 Unit cell: (149.597, 149.597, 118.19, 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 176 16.00 P 80 15.00 O 6216 8.00 N 5376 7.00 C 19544 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.5 seconds 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7264 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 44 sheets defined 36.7% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.533A pdb=" N GLN A 48 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 49 " --> pdb=" O ALA A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 49' Processing helix chain 'A' and resid 75 through 85 removed outlier: 3.770A pdb=" N THR A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.973A pdb=" N VAL A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.598A pdb=" N ASP A 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) 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 removed outlier: 3.511A pdb=" N ALA A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 255 through 267 removed outlier: 4.144A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.745A pdb=" N LYS A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 336 removed outlier: 3.559A pdb=" N VAL A 336 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.837A pdb=" N ILE A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 496 through 502 removed outlier: 3.876A pdb=" N GLY A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.533A pdb=" N GLN B 48 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 49 " --> pdb=" O ALA B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 49' Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.770A pdb=" N THR B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 126 through 138 removed outlier: 3.973A pdb=" N VAL B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 removed outlier: 3.598A pdb=" N ASP B 162 " --> pdb=" O SER B 159 " (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: 3.511A pdb=" N ALA B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 255 through 267 removed outlier: 4.144A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 291 Processing helix chain 'B' and resid 307 through 315 removed outlier: 3.745A pdb=" N LYS B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 336 removed outlier: 3.559A pdb=" N VAL B 336 " --> pdb=" O THR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.837A pdb=" N ILE B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 472 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 496 through 502 removed outlier: 3.875A pdb=" N GLY B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.533A pdb=" N GLN C 48 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 49 " --> pdb=" O ALA C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 49' Processing helix chain 'C' and resid 75 through 85 removed outlier: 3.770A pdb=" N THR C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 126 through 138 removed outlier: 3.973A pdb=" N VAL C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.599A pdb=" N ASP C 162 " --> pdb=" O SER C 159 " (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: 3.512A pdb=" N ALA C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 255 through 267 removed outlier: 4.144A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 291 Processing helix chain 'C' and resid 307 through 315 removed outlier: 3.746A pdb=" N LYS C 311 " --> pdb=" O ALA C 307 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.560A pdb=" N VAL C 336 " --> pdb=" O THR C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.836A pdb=" N ILE C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 380 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 472 Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 496 through 502 removed outlier: 3.875A pdb=" N GLY C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 45 through 49 removed outlier: 3.534A pdb=" N GLN D 48 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 49 " --> pdb=" O ALA D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 49' Processing helix chain 'D' and resid 75 through 85 removed outlier: 3.769A pdb=" N THR D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 126 through 138 removed outlier: 3.974A pdb=" N VAL D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.598A pdb=" N ASP D 162 " --> pdb=" O SER D 159 " (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: 3.512A pdb=" N ALA D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 255 through 267 removed outlier: 4.144A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 291 Processing helix chain 'D' and resid 307 through 315 removed outlier: 3.746A pdb=" N LYS D 311 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 336 removed outlier: 3.560A pdb=" N VAL D 336 " --> pdb=" O THR D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.838A pdb=" N ILE D 373 " --> pdb=" O ASN D 369 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY D 380 " --> pdb=" O ALA D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 472 Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 496 through 502 removed outlier: 3.875A pdb=" N GLY D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.533A pdb=" N GLN E 48 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.570A 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: 3.770A pdb=" N THR E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 126 through 138 removed outlier: 3.973A pdb=" N VAL E 130 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 removed outlier: 3.598A pdb=" N ASP E 162 " --> pdb=" O SER E 159 " (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 removed outlier: 3.510A pdb=" N ALA E 197 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 255 through 267 removed outlier: 4.144A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 291 Processing helix chain 'E' and resid 307 through 315 removed outlier: 3.745A pdb=" N LYS E 311 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 336 removed outlier: 3.560A pdb=" N VAL E 336 " --> pdb=" O THR E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 369 through 380 removed outlier: 3.837A pdb=" N ILE E 373 " --> pdb=" O ASN E 369 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY E 380 " --> pdb=" O ALA E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 472 Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 496 through 502 removed outlier: 3.875A pdb=" N GLY E 502 " --> pdb=" O GLN E 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 45 through 49 removed outlier: 3.533A pdb=" N GLN F 48 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 3.569A 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: 3.771A pdb=" N THR F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 126 through 138 removed outlier: 3.972A pdb=" N VAL F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.599A pdb=" N ASP F 162 " --> pdb=" O SER F 159 " (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 removed outlier: 3.511A pdb=" N ALA F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 233 Processing helix chain 'F' and resid 255 through 267 removed outlier: 4.144A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP F 261 " --> pdb=" O LYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 291 Processing helix chain 'F' and resid 307 through 315 removed outlier: 3.745A pdb=" N LYS F 311 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 336 removed outlier: 3.560A pdb=" N VAL F 336 " --> pdb=" O THR F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 369 through 380 removed outlier: 3.837A pdb=" N ILE F 373 " --> pdb=" O ASN F 369 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY F 380 " --> pdb=" O ALA F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 472 Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 496 through 502 removed outlier: 3.876A pdb=" N GLY F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 45 through 49 removed outlier: 3.533A pdb=" N GLN G 48 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 3.570A 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: 3.771A pdb=" N THR G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 126 through 138 removed outlier: 3.973A pdb=" N VAL G 130 " --> pdb=" O ARG G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 removed outlier: 3.598A pdb=" N ASP G 162 " --> pdb=" O SER G 159 " (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 removed outlier: 3.511A pdb=" N ALA G 197 " --> pdb=" O THR G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 233 Processing helix chain 'G' and resid 255 through 267 removed outlier: 4.144A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP G 261 " --> pdb=" O LYS G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 291 Processing helix chain 'G' and resid 307 through 315 removed outlier: 3.745A pdb=" N LYS G 311 " --> pdb=" O ALA G 307 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 336 removed outlier: 3.561A pdb=" N VAL G 336 " --> pdb=" O THR G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 369 through 380 removed outlier: 3.837A pdb=" N ILE G 373 " --> pdb=" O ASN G 369 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY G 380 " --> pdb=" O ALA G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 456 through 472 Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 496 through 502 removed outlier: 3.876A pdb=" N GLY G 502 " --> pdb=" O GLN G 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 24 Processing helix chain 'H' and resid 45 through 49 removed outlier: 3.533A pdb=" N GLN H 48 " --> pdb=" O THR H 45 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL H 49 " --> pdb=" O ALA H 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 45 through 49' Processing helix chain 'H' and resid 75 through 85 removed outlier: 3.770A pdb=" N THR H 85 " --> pdb=" O ALA H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 126 through 138 removed outlier: 3.972A pdb=" N VAL H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 163 removed outlier: 3.598A pdb=" N ASP H 162 " --> pdb=" O SER H 159 " (cutoff:3.500A) 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 removed outlier: 3.512A pdb=" N ALA H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 255 through 267 removed outlier: 4.144A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP H 261 " --> pdb=" O LYS H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 291 Processing helix chain 'H' and resid 307 through 315 removed outlier: 3.746A pdb=" N LYS H 311 " --> pdb=" O ALA H 307 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 336 removed outlier: 3.560A pdb=" N VAL H 336 " --> pdb=" O THR H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 355 Processing helix chain 'H' and resid 369 through 380 removed outlier: 3.837A pdb=" N ILE H 373 " --> pdb=" O ASN H 369 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY H 380 " --> pdb=" O ALA H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 472 Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 496 through 502 removed outlier: 3.875A pdb=" N GLY H 502 " --> pdb=" O GLN H 498 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 6 removed outlier: 3.794A pdb=" N ILE I 6 " --> pdb=" O ALA I 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2 through 6' Processing helix chain 'J' and resid 2 through 6 removed outlier: 3.794A pdb=" N ILE J 6 " --> pdb=" O ALA J 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 2 through 6' Processing helix chain 'K' and resid 2 through 6 removed outlier: 3.794A 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 'L' and resid 2 through 6 removed outlier: 3.794A 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 'M' and resid 2 through 6 removed outlier: 3.794A pdb=" N ILE M 6 " --> pdb=" O ALA M 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 2 through 6' Processing helix chain 'N' and resid 2 through 6 removed outlier: 3.794A pdb=" N ILE N 6 " --> pdb=" O ALA N 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 2 through 6' Processing helix chain 'O' and resid 2 through 6 removed outlier: 3.794A pdb=" N ILE O 6 " --> pdb=" O ALA O 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 2 through 6' Processing helix chain 'P' and resid 2 through 6 removed outlier: 3.794A pdb=" N ILE P 6 " --> pdb=" O ALA P 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 2 through 6' 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 removed outlier: 3.507A pdb=" N SER A 53 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 4.017A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY A 89 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA A 249 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 299 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 5.921A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 400 through 403 removed outlier: 3.547A pdb=" N SER A 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 509 through 511 removed outlier: 3.546A pdb=" N SER B 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER F 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.507A pdb=" N SER B 53 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 67 removed outlier: 4.017A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY B 89 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA B 249 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 299 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.624A pdb=" N GLY B 156 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 188 through 189 removed outlier: 5.921A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 509 through 511 removed outlier: 3.549A pdb=" N SER C 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.508A pdb=" N SER C 53 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 67 removed outlier: 4.017A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLY C 89 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA C 249 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL C 299 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 188 through 189 removed outlier: 5.921A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 509 through 511 removed outlier: 3.580A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER H 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.508A pdb=" N SER D 53 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 67 removed outlier: 4.018A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLY D 89 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA D 249 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL D 299 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 188 through 189 removed outlier: 5.921A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.507A pdb=" N SER E 53 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 67 removed outlier: 4.017A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY E 89 " --> pdb=" O GLY E 247 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA E 249 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL E 299 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY E 156 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 188 through 189 removed outlier: 5.921A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD4, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.507A pdb=" N SER F 53 " --> pdb=" O LEU F 61 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 65 through 67 removed outlier: 4.018A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY F 89 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA F 249 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE F 91 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL F 299 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ARG F 322 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY F 301 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 188 through 189 removed outlier: 5.920A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AD9, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.507A pdb=" N SER G 53 " --> pdb=" O LEU G 61 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 65 through 67 removed outlier: 4.018A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY G 89 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA G 249 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL G 299 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY G 156 " --> pdb=" O ILE G 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 188 through 189 removed outlier: 5.921A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE5, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.507A pdb=" N SER H 53 " --> pdb=" O LEU H 61 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 65 through 67 removed outlier: 4.017A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY H 89 " --> pdb=" O GLY H 247 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA H 249 " --> pdb=" O GLY H 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL H 299 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 188 through 189 removed outlier: 5.921A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 1032 hydrogen bonds defined for protein. 2952 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: 7.35 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 5288 1.30 - 1.43: 7628 1.43 - 1.56: 18510 1.56 - 1.68: 206 1.68 - 1.81: 288 Bond restraints: 31920 Sorted by residual: bond pdb=" C2' GTP G 603 " pdb=" C3' GTP G 603 " ideal model delta sigma weight residual 1.524 1.231 0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C2' GTP E 603 " pdb=" C3' GTP E 603 " ideal model delta sigma weight residual 1.524 1.231 0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C2' GTP C 603 " pdb=" C3' GTP C 603 " ideal model delta sigma weight residual 1.524 1.231 0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C2' GTP A 603 " pdb=" C3' GTP A 603 " ideal model delta sigma weight residual 1.524 1.231 0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C2' GTP D 603 " pdb=" C3' GTP D 603 " ideal model delta sigma weight residual 1.524 1.231 0.293 2.00e-02 2.50e+03 2.14e+02 ... (remaining 31915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 42649 3.97 - 7.94: 543 7.94 - 11.90: 80 11.90 - 15.87: 8 15.87 - 19.84: 8 Bond angle restraints: 43288 Sorted by residual: angle pdb=" PB ATP F 604 " pdb=" O3B ATP F 604 " pdb=" PG ATP F 604 " ideal model delta sigma weight residual 139.87 120.03 19.84 1.00e+00 1.00e+00 3.94e+02 angle pdb=" PB ATP H 604 " pdb=" O3B ATP H 604 " pdb=" PG ATP H 604 " ideal model delta sigma weight residual 139.87 120.05 19.82 1.00e+00 1.00e+00 3.93e+02 angle pdb=" PB ATP A 604 " pdb=" O3B ATP A 604 " pdb=" PG ATP A 604 " ideal model delta sigma weight residual 139.87 120.05 19.82 1.00e+00 1.00e+00 3.93e+02 angle pdb=" PB ATP D 604 " pdb=" O3B ATP D 604 " pdb=" PG ATP D 604 " ideal model delta sigma weight residual 139.87 120.07 19.80 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PB ATP G 604 " pdb=" O3B ATP G 604 " pdb=" PG ATP G 604 " ideal model delta sigma weight residual 139.87 120.07 19.80 1.00e+00 1.00e+00 3.92e+02 ... (remaining 43283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 18927 34.22 - 68.43: 341 68.43 - 102.65: 24 102.65 - 136.86: 8 136.86 - 171.08: 36 Dihedral angle restraints: 19336 sinusoidal: 7952 harmonic: 11384 Sorted by residual: dihedral pdb=" O2G GTP H 602 " pdb=" O3B GTP H 602 " pdb=" PG GTP H 602 " pdb=" PB GTP H 602 " ideal model delta sinusoidal sigma weight residual 177.30 6.22 171.08 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2G GTP D 602 " pdb=" O3B GTP D 602 " pdb=" PG GTP D 602 " pdb=" PB GTP D 602 " ideal model delta sinusoidal sigma weight residual 177.30 6.23 171.07 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2G GTP C 602 " pdb=" O3B GTP C 602 " pdb=" PG GTP C 602 " pdb=" PB GTP C 602 " ideal model delta sinusoidal sigma weight residual 177.30 6.24 171.06 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 19333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3071 0.050 - 0.101: 1411 0.101 - 0.151: 390 0.151 - 0.202: 48 0.202 - 0.252: 8 Chirality restraints: 4928 Sorted by residual: chirality pdb=" CB THR A 74 " pdb=" CA THR A 74 " pdb=" OG1 THR A 74 " pdb=" CG2 THR A 74 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB THR B 74 " pdb=" CA THR B 74 " pdb=" OG1 THR B 74 " pdb=" CG2 THR B 74 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB THR C 74 " pdb=" CA THR C 74 " pdb=" OG1 THR C 74 " pdb=" CG2 THR C 74 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 4925 not shown) Planarity restraints: 5424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN F 334 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" CD GLN F 334 " 0.038 2.00e-02 2.50e+03 pdb=" OE1 GLN F 334 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN F 334 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 334 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" CD GLN G 334 " 0.038 2.00e-02 2.50e+03 pdb=" OE1 GLN G 334 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN G 334 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 334 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.81e+00 pdb=" CD GLN A 334 " -0.038 2.00e-02 2.50e+03 pdb=" OE1 GLN A 334 " 0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN A 334 " 0.013 2.00e-02 2.50e+03 ... (remaining 5421 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 8722 2.81 - 3.33: 28092 3.33 - 3.85: 51643 3.85 - 4.38: 61731 4.38 - 4.90: 104651 Nonbonded interactions: 254839 Sorted by model distance: nonbonded pdb=" OG SER A 327 " pdb=" OE1 GLN A 343 " model vdw 2.284 3.040 nonbonded pdb=" OG SER E 327 " pdb=" OE1 GLN E 343 " model vdw 2.284 3.040 nonbonded pdb=" OG SER D 327 " pdb=" OE1 GLN D 343 " model vdw 2.285 3.040 nonbonded pdb=" OG SER F 327 " pdb=" OE1 GLN F 343 " model vdw 2.285 3.040 nonbonded pdb=" OG SER C 327 " pdb=" OE1 GLN C 343 " model vdw 2.285 3.040 ... (remaining 254834 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 4.230 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: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 29.830 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.120 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:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 0.293 31928 Z= 0.709 Angle : 1.229 19.841 43288 Z= 0.737 Chirality : 0.059 0.252 4928 Planarity : 0.006 0.046 5424 Dihedral : 15.770 171.080 12072 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.21 % Allowed : 5.15 % Favored : 92.65 % 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: -4.03 (0.10), residues: 3960 helix: -3.27 (0.09), residues: 1312 sheet: -2.33 (0.18), residues: 544 loop : -2.33 (0.12), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 355 TYR 0.031 0.003 TYR F 484 PHE 0.015 0.003 PHE C 401 HIS 0.005 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.01428 (31920) covalent geometry : angle 1.22942 (43288) hydrogen bonds : bond 0.20158 ( 1032) hydrogen bonds : angle 8.52875 ( 2952) Misc. bond : bond 0.00183 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 816 time to evaluate : 1.212 Fit side-chains REVERT: A 105 ARG cc_start: 0.7351 (mtp-110) cc_final: 0.6953 (ttt-90) REVERT: A 149 ARG cc_start: 0.6430 (mpp-170) cc_final: 0.6197 (mpt180) REVERT: A 170 GLU cc_start: 0.2783 (OUTLIER) cc_final: 0.2321 (mp0) REVERT: A 203 ARG cc_start: 0.7818 (mpt90) cc_final: 0.7116 (mtm110) REVERT: A 228 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7531 (ptmm) REVERT: A 232 ASP cc_start: 0.8604 (m-30) cc_final: 0.8360 (m-30) REVERT: A 235 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.6933 (pp) REVERT: A 410 LYS cc_start: 0.7570 (pttt) cc_final: 0.6363 (mmtt) REVERT: A 509 TYR cc_start: 0.8038 (p90) cc_final: 0.7683 (p90) REVERT: B 105 ARG cc_start: 0.7322 (mtp-110) cc_final: 0.6913 (ttt-90) REVERT: B 149 ARG cc_start: 0.6484 (mpp-170) cc_final: 0.6136 (mpt180) REVERT: B 170 GLU cc_start: 0.2801 (OUTLIER) cc_final: 0.2182 (mp0) REVERT: B 203 ARG cc_start: 0.7831 (mpt90) cc_final: 0.7033 (mtm110) REVERT: B 228 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7446 (ptmm) REVERT: B 232 ASP cc_start: 0.8551 (m-30) cc_final: 0.8345 (m-30) REVERT: B 235 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.6708 (pp) REVERT: B 408 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6721 (pp) REVERT: B 410 LYS cc_start: 0.7600 (pttt) cc_final: 0.6227 (mmtt) REVERT: B 509 TYR cc_start: 0.8074 (p90) cc_final: 0.7768 (p90) REVERT: C 13 VAL cc_start: 0.8678 (t) cc_final: 0.8437 (p) REVERT: C 105 ARG cc_start: 0.7364 (mtp-110) cc_final: 0.6973 (ttt-90) REVERT: C 149 ARG cc_start: 0.6465 (mpp-170) cc_final: 0.6263 (mpt180) REVERT: C 170 GLU cc_start: 0.2860 (OUTLIER) cc_final: 0.2377 (mp0) REVERT: C 203 ARG cc_start: 0.7823 (mpt90) cc_final: 0.7023 (mtm110) REVERT: C 228 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7424 (ptmm) REVERT: C 232 ASP cc_start: 0.8600 (m-30) cc_final: 0.8330 (m-30) REVERT: C 235 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.6948 (pp) REVERT: C 408 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6595 (pp) REVERT: C 410 LYS cc_start: 0.7638 (pttt) cc_final: 0.6331 (mmtt) REVERT: C 509 TYR cc_start: 0.8068 (p90) cc_final: 0.7687 (p90) REVERT: D 13 VAL cc_start: 0.8552 (t) cc_final: 0.8272 (p) REVERT: D 149 ARG cc_start: 0.6472 (mpp-170) cc_final: 0.6148 (mpt180) REVERT: D 170 GLU cc_start: 0.2645 (OUTLIER) cc_final: 0.2219 (mp0) REVERT: D 203 ARG cc_start: 0.7769 (mpt90) cc_final: 0.6930 (mtm110) REVERT: D 228 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7502 (ptmm) REVERT: D 232 ASP cc_start: 0.8530 (m-30) cc_final: 0.8314 (m-30) REVERT: D 235 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6668 (pp) REVERT: D 408 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6704 (pp) REVERT: D 410 LYS cc_start: 0.7646 (pttt) cc_final: 0.6218 (mmtt) REVERT: D 509 TYR cc_start: 0.8094 (p90) cc_final: 0.7768 (p90) REVERT: E 105 ARG cc_start: 0.7340 (mtp-110) cc_final: 0.6909 (ttt-90) REVERT: E 170 GLU cc_start: 0.2708 (OUTLIER) cc_final: 0.2186 (mp0) REVERT: E 203 ARG cc_start: 0.7886 (mpt90) cc_final: 0.7159 (mtm110) REVERT: E 228 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7425 (ptmm) REVERT: E 232 ASP cc_start: 0.8580 (m-30) cc_final: 0.8333 (m-30) REVERT: E 235 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.6899 (pp) REVERT: E 386 MET cc_start: 0.8472 (mtm) cc_final: 0.8214 (mtp) REVERT: E 408 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6547 (pp) REVERT: E 410 LYS cc_start: 0.7557 (pttt) cc_final: 0.6356 (mmtt) REVERT: E 509 TYR cc_start: 0.8085 (p90) cc_final: 0.7689 (p90) REVERT: F 13 VAL cc_start: 0.8574 (t) cc_final: 0.8301 (p) REVERT: F 149 ARG cc_start: 0.6561 (mpp-170) cc_final: 0.6261 (mpt180) REVERT: F 170 GLU cc_start: 0.2675 (OUTLIER) cc_final: 0.2036 (mp0) REVERT: F 203 ARG cc_start: 0.7799 (mpt90) cc_final: 0.6969 (mtm110) REVERT: F 228 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7381 (ptmm) REVERT: F 232 ASP cc_start: 0.8534 (m-30) cc_final: 0.8326 (m-30) REVERT: F 235 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.6676 (pp) REVERT: F 408 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6669 (pp) REVERT: F 410 LYS cc_start: 0.7663 (pttt) cc_final: 0.6259 (mmtt) REVERT: F 509 TYR cc_start: 0.8097 (p90) cc_final: 0.7771 (p90) REVERT: G 149 ARG cc_start: 0.6461 (mpp-170) cc_final: 0.6217 (mpt180) REVERT: G 170 GLU cc_start: 0.2585 (OUTLIER) cc_final: 0.2064 (mp0) REVERT: G 203 ARG cc_start: 0.7798 (mpt90) cc_final: 0.7197 (mtp180) REVERT: G 228 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7415 (ptmm) REVERT: G 232 ASP cc_start: 0.8563 (m-30) cc_final: 0.8308 (m-30) REVERT: G 235 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.6895 (pp) REVERT: G 410 LYS cc_start: 0.7576 (pttt) cc_final: 0.6346 (mmtt) REVERT: G 509 TYR cc_start: 0.8072 (p90) cc_final: 0.7667 (p90) REVERT: H 13 VAL cc_start: 0.8555 (t) cc_final: 0.8291 (p) REVERT: H 105 ARG cc_start: 0.7286 (mtp-110) cc_final: 0.6862 (ttt-90) REVERT: H 149 ARG cc_start: 0.6365 (mpp-170) cc_final: 0.6062 (mpt180) REVERT: H 170 GLU cc_start: 0.2727 (OUTLIER) cc_final: 0.2151 (mp0) REVERT: H 203 ARG cc_start: 0.7873 (mpt90) cc_final: 0.7034 (mtm110) REVERT: H 228 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7506 (ptmm) REVERT: H 235 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.6695 (pp) REVERT: H 401 PHE cc_start: 0.7896 (p90) cc_final: 0.7521 (p90) REVERT: H 408 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6727 (pp) REVERT: H 410 LYS cc_start: 0.7624 (pttt) cc_final: 0.6287 (mmtt) REVERT: H 509 TYR cc_start: 0.8078 (p90) cc_final: 0.7751 (p90) outliers start: 72 outliers final: 20 residues processed: 856 average time/residue: 0.2023 time to fit residues: 277.5120 Evaluate side-chains 600 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 550 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 228 LYS Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 228 LYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 228 LYS Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 0.0570 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 48 GLN A 198 ASN A 253 HIS A 298 GLN ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN A 504 HIS A 507 HIS B 48 GLN B 198 ASN B 253 HIS B 298 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 498 GLN B 504 HIS B 507 HIS C 48 GLN C 198 ASN C 253 HIS C 298 GLN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN C 504 HIS C 507 HIS D 48 GLN D 112 GLN D 198 ASN D 253 HIS D 298 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 498 GLN D 504 HIS D 507 HIS E 25 ASN E 48 GLN E 198 ASN E 253 HIS E 298 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN E 504 HIS E 507 HIS F 48 GLN F 198 ASN F 253 HIS F 298 GLN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN F 498 GLN F 504 HIS F 507 HIS G 25 ASN G 48 GLN G 112 GLN G 198 ASN G 253 HIS G 298 GLN ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN G 498 GLN G 504 HIS G 507 HIS H 48 GLN H 112 GLN H 198 ASN H 253 HIS H 298 GLN ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 504 HIS H 507 HIS Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.158837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122826 restraints weight = 36123.432| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.43 r_work: 0.3260 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31928 Z= 0.119 Angle : 0.583 6.627 43288 Z= 0.294 Chirality : 0.044 0.159 4928 Planarity : 0.004 0.041 5424 Dihedral : 18.315 176.036 4995 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.70 % Allowed : 10.72 % Favored : 86.58 % 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: -2.67 (0.12), residues: 3960 helix: -1.46 (0.12), residues: 1344 sheet: -1.93 (0.19), residues: 544 loop : -1.91 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 407 TYR 0.016 0.001 TYR H 353 PHE 0.006 0.001 PHE G 402 HIS 0.001 0.000 HIS F 253 Details of bonding type rmsd covalent geometry : bond 0.00265 (31920) covalent geometry : angle 0.58345 (43288) hydrogen bonds : bond 0.03146 ( 1032) hydrogen bonds : angle 5.35088 ( 2952) Misc. bond : bond 0.00019 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 616 time to evaluate : 1.063 Fit side-chains REVERT: A 105 ARG cc_start: 0.7336 (mtp-110) cc_final: 0.6820 (ttp80) REVERT: A 170 GLU cc_start: 0.3594 (OUTLIER) cc_final: 0.2985 (tp30) REVERT: A 203 ARG cc_start: 0.7745 (mpt90) cc_final: 0.7007 (mtp180) REVERT: A 232 ASP cc_start: 0.8769 (m-30) cc_final: 0.8301 (m-30) REVERT: A 235 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.6835 (pp) REVERT: A 261 ASP cc_start: 0.8286 (t70) cc_final: 0.7463 (m-30) REVERT: A 330 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8998 (pp) REVERT: A 351 SER cc_start: 0.8367 (t) cc_final: 0.7962 (m) REVERT: A 410 LYS cc_start: 0.7175 (pttt) cc_final: 0.5843 (mmtt) REVERT: A 487 GLU cc_start: 0.8599 (tt0) cc_final: 0.8341 (tt0) REVERT: A 509 TYR cc_start: 0.8054 (p90) cc_final: 0.7440 (p90) REVERT: B 105 ARG cc_start: 0.7304 (mtp-110) cc_final: 0.6773 (ttp80) REVERT: B 149 ARG cc_start: 0.5863 (mpp-170) cc_final: 0.5570 (mpt180) REVERT: B 170 GLU cc_start: 0.3341 (OUTLIER) cc_final: 0.2504 (tp30) REVERT: B 203 ARG cc_start: 0.7823 (mpt90) cc_final: 0.6997 (mtm110) REVERT: B 217 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5870 (mm-30) REVERT: B 228 LYS cc_start: 0.7183 (ptmm) cc_final: 0.6881 (ptmm) REVERT: B 232 ASP cc_start: 0.8715 (m-30) cc_final: 0.8368 (m-30) REVERT: B 235 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.6500 (pp) REVERT: B 261 ASP cc_start: 0.8141 (t70) cc_final: 0.7287 (m-30) REVERT: B 327 SER cc_start: 0.8941 (p) cc_final: 0.8662 (t) REVERT: B 351 SER cc_start: 0.8443 (t) cc_final: 0.8039 (m) REVERT: B 410 LYS cc_start: 0.7329 (pttt) cc_final: 0.5914 (mmtt) REVERT: B 509 TYR cc_start: 0.8094 (p90) cc_final: 0.7530 (p90) REVERT: C 105 ARG cc_start: 0.7359 (mtp-110) cc_final: 0.6819 (ttp80) REVERT: C 149 ARG cc_start: 0.5896 (mpp-170) cc_final: 0.5614 (mpt180) REVERT: C 165 PHE cc_start: 0.8287 (m-80) cc_final: 0.8025 (m-80) REVERT: C 170 GLU cc_start: 0.3646 (OUTLIER) cc_final: 0.2630 (tp30) REVERT: C 203 ARG cc_start: 0.7671 (mpt90) cc_final: 0.6938 (mtp180) REVERT: C 232 ASP cc_start: 0.8700 (m-30) cc_final: 0.8207 (m-30) REVERT: C 235 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.6709 (pp) REVERT: C 257 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7982 (mtmt) REVERT: C 261 ASP cc_start: 0.8261 (t70) cc_final: 0.7448 (m-30) REVERT: C 351 SER cc_start: 0.8427 (t) cc_final: 0.8033 (m) REVERT: C 410 LYS cc_start: 0.7362 (pttt) cc_final: 0.6055 (mmtt) REVERT: C 509 TYR cc_start: 0.8087 (p90) cc_final: 0.7439 (p90) REVERT: D 16 ASP cc_start: 0.8555 (t70) cc_final: 0.8139 (t0) REVERT: D 149 ARG cc_start: 0.5934 (mpp-170) cc_final: 0.5617 (mpt180) REVERT: D 170 GLU cc_start: 0.3472 (OUTLIER) cc_final: 0.2689 (tp30) REVERT: D 203 ARG cc_start: 0.7696 (mpt90) cc_final: 0.6916 (mtp180) REVERT: D 217 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5837 (mm-30) REVERT: D 228 LYS cc_start: 0.7195 (ptmm) cc_final: 0.6962 (ptmm) REVERT: D 232 ASP cc_start: 0.8696 (m-30) cc_final: 0.8383 (m-30) REVERT: D 235 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.6496 (pp) REVERT: D 261 ASP cc_start: 0.8137 (t70) cc_final: 0.7270 (m-30) REVERT: D 327 SER cc_start: 0.8943 (p) cc_final: 0.8650 (t) REVERT: D 351 SER cc_start: 0.8448 (t) cc_final: 0.8045 (m) REVERT: D 410 LYS cc_start: 0.7443 (pttt) cc_final: 0.5984 (mmtt) REVERT: D 487 GLU cc_start: 0.8617 (tt0) cc_final: 0.8416 (tt0) REVERT: D 509 TYR cc_start: 0.8078 (p90) cc_final: 0.7460 (p90) REVERT: E 105 ARG cc_start: 0.7305 (mtp-110) cc_final: 0.6727 (ttp80) REVERT: E 149 ARG cc_start: 0.6112 (mpt180) cc_final: 0.5766 (mpt180) REVERT: E 170 GLU cc_start: 0.3387 (OUTLIER) cc_final: 0.2485 (tp30) REVERT: E 203 ARG cc_start: 0.7760 (mpt90) cc_final: 0.7044 (mtp180) REVERT: E 232 ASP cc_start: 0.8715 (m-30) cc_final: 0.8212 (m-30) REVERT: E 235 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.6761 (pp) REVERT: E 261 ASP cc_start: 0.8241 (t70) cc_final: 0.7441 (m-30) REVERT: E 330 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8935 (pp) REVERT: E 351 SER cc_start: 0.8413 (t) cc_final: 0.7998 (m) REVERT: E 410 LYS cc_start: 0.7294 (pttt) cc_final: 0.6061 (mmtt) REVERT: F 149 ARG cc_start: 0.5903 (mpp-170) cc_final: 0.5572 (mpt180) REVERT: F 170 GLU cc_start: 0.3332 (OUTLIER) cc_final: 0.2691 (tp30) REVERT: F 196 GLU cc_start: 0.7402 (mp0) cc_final: 0.6956 (mt-10) REVERT: F 203 ARG cc_start: 0.7765 (mpt90) cc_final: 0.7002 (mtp180) REVERT: F 217 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.5871 (mm-30) REVERT: F 232 ASP cc_start: 0.8662 (m-30) cc_final: 0.8260 (m-30) REVERT: F 235 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.6525 (pp) REVERT: F 261 ASP cc_start: 0.8117 (t70) cc_final: 0.7262 (m-30) REVERT: F 327 SER cc_start: 0.8968 (p) cc_final: 0.8661 (t) REVERT: F 351 SER cc_start: 0.8445 (t) cc_final: 0.8049 (m) REVERT: F 410 LYS cc_start: 0.7414 (pttt) cc_final: 0.6011 (mmtt) REVERT: F 509 TYR cc_start: 0.8060 (p90) cc_final: 0.7453 (p90) REVERT: G 170 GLU cc_start: 0.3431 (OUTLIER) cc_final: 0.2833 (tp30) REVERT: G 203 ARG cc_start: 0.7680 (mpt90) cc_final: 0.6975 (mtp180) REVERT: G 232 ASP cc_start: 0.8695 (m-30) cc_final: 0.8215 (m-30) REVERT: G 235 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.6773 (pp) REVERT: G 257 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7860 (mttt) REVERT: G 261 ASP cc_start: 0.8243 (t70) cc_final: 0.7427 (m-30) REVERT: G 351 SER cc_start: 0.8342 (t) cc_final: 0.7959 (m) REVERT: G 386 MET cc_start: 0.9245 (mtm) cc_final: 0.9004 (mtp) REVERT: G 410 LYS cc_start: 0.7215 (pttt) cc_final: 0.5883 (mmtt) REVERT: G 487 GLU cc_start: 0.8567 (tt0) cc_final: 0.8367 (tt0) REVERT: H 105 ARG cc_start: 0.7235 (mtp-110) cc_final: 0.6680 (ttp80) REVERT: H 149 ARG cc_start: 0.5783 (mpp-170) cc_final: 0.5511 (mpt180) REVERT: H 170 GLU cc_start: 0.3378 (OUTLIER) cc_final: 0.2456 (tp30) REVERT: H 196 GLU cc_start: 0.7529 (mp0) cc_final: 0.7070 (mt-10) REVERT: H 217 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.5943 (mm-30) REVERT: H 235 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.6506 (pp) REVERT: H 261 ASP cc_start: 0.8112 (t70) cc_final: 0.7215 (m-30) REVERT: H 327 SER cc_start: 0.8985 (p) cc_final: 0.8688 (t) REVERT: H 351 SER cc_start: 0.8406 (t) cc_final: 0.7989 (m) REVERT: H 410 LYS cc_start: 0.7394 (pttt) cc_final: 0.6055 (mmtt) REVERT: H 459 TYR cc_start: 0.8779 (t80) cc_final: 0.8572 (t80) REVERT: H 509 TYR cc_start: 0.8045 (p90) cc_final: 0.7446 (p90) REVERT: P 5 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8331 (mp) outliers start: 88 outliers final: 43 residues processed: 680 average time/residue: 0.1916 time to fit residues: 211.3962 Evaluate side-chains 576 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 510 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 485 SER Chi-restraints excluded: chain P residue 5 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 223 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 263 optimal weight: 5.9990 chunk 25 optimal weight: 0.2980 chunk 306 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 317 optimal weight: 0.9980 chunk 346 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN A 334 GLN B 243 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN C 334 GLN D 112 GLN D 243 GLN D 334 GLN E 48 GLN E 243 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN F 334 GLN G 112 GLN G 243 GLN G 334 GLN H 112 GLN H 243 GLN H 334 GLN H 498 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.160349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124273 restraints weight = 36162.236| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.42 r_work: 0.3256 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 31928 Z= 0.107 Angle : 0.544 6.523 43288 Z= 0.273 Chirality : 0.043 0.135 4928 Planarity : 0.004 0.039 5424 Dihedral : 17.425 178.075 4925 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.28 % Allowed : 11.61 % Favored : 85.11 % 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: -1.75 (0.12), residues: 3960 helix: -0.30 (0.14), residues: 1328 sheet: -1.48 (0.21), residues: 544 loop : -1.63 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 493 TYR 0.014 0.001 TYR E 509 PHE 0.011 0.001 PHE H 402 HIS 0.001 0.000 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00249 (31920) covalent geometry : angle 0.54420 (43288) hydrogen bonds : bond 0.02717 ( 1032) hydrogen bonds : angle 4.77072 ( 2952) Misc. bond : bond 0.00030 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 565 time to evaluate : 1.116 Fit side-chains REVERT: A 105 ARG cc_start: 0.7310 (mtp-110) cc_final: 0.6755 (ttp80) REVERT: A 149 ARG cc_start: 0.6054 (mpt180) cc_final: 0.5583 (mpt180) REVERT: A 170 GLU cc_start: 0.3693 (OUTLIER) cc_final: 0.2574 (tp30) REVERT: A 196 GLU cc_start: 0.7581 (mp0) cc_final: 0.7127 (mt-10) REVERT: A 203 ARG cc_start: 0.7793 (mpt90) cc_final: 0.7000 (mtp180) REVERT: A 232 ASP cc_start: 0.8636 (m-30) cc_final: 0.8238 (m-30) REVERT: A 235 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.6719 (pp) REVERT: A 261 ASP cc_start: 0.8362 (t0) cc_final: 0.7614 (m-30) REVERT: A 286 MET cc_start: 0.8747 (tpp) cc_final: 0.8132 (tpt) REVERT: A 330 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8967 (pp) REVERT: A 351 SER cc_start: 0.8322 (t) cc_final: 0.7928 (m) REVERT: A 410 LYS cc_start: 0.7278 (pttt) cc_final: 0.6008 (mmtt) REVERT: B 105 ARG cc_start: 0.7298 (mtp-110) cc_final: 0.6757 (ttp80) REVERT: B 170 GLU cc_start: 0.3583 (OUTLIER) cc_final: 0.2449 (tp30) REVERT: B 196 GLU cc_start: 0.7605 (mp0) cc_final: 0.7150 (mt-10) REVERT: B 203 ARG cc_start: 0.7766 (mpt90) cc_final: 0.6819 (mtm110) REVERT: B 217 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5839 (mm-30) REVERT: B 232 ASP cc_start: 0.8647 (m-30) cc_final: 0.8202 (m-30) REVERT: B 235 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6467 (pp) REVERT: B 257 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7838 (mttt) REVERT: B 261 ASP cc_start: 0.8241 (t0) cc_final: 0.7447 (m-30) REVERT: B 286 MET cc_start: 0.8764 (tpp) cc_final: 0.8211 (tpt) REVERT: B 330 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8842 (pp) REVERT: B 351 SER cc_start: 0.8408 (t) cc_final: 0.8007 (m) REVERT: B 410 LYS cc_start: 0.7311 (pttt) cc_final: 0.5940 (mmtt) REVERT: B 509 TYR cc_start: 0.8193 (p90) cc_final: 0.7608 (p90) REVERT: C 13 VAL cc_start: 0.8555 (t) cc_final: 0.8248 (p) REVERT: C 105 ARG cc_start: 0.7349 (mtp-110) cc_final: 0.6804 (ttp80) REVERT: C 149 ARG cc_start: 0.5954 (mpp-170) cc_final: 0.5597 (mpt180) REVERT: C 170 GLU cc_start: 0.3807 (OUTLIER) cc_final: 0.2488 (tp30) REVERT: C 196 GLU cc_start: 0.7401 (mp0) cc_final: 0.6928 (mt-10) REVERT: C 203 ARG cc_start: 0.7723 (mpt90) cc_final: 0.6978 (mtp180) REVERT: C 232 ASP cc_start: 0.8572 (m-30) cc_final: 0.8159 (m-30) REVERT: C 235 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.6712 (pp) REVERT: C 261 ASP cc_start: 0.8323 (t0) cc_final: 0.7574 (m-30) REVERT: C 286 MET cc_start: 0.8779 (tpp) cc_final: 0.8179 (tpt) REVERT: C 351 SER cc_start: 0.8329 (t) cc_final: 0.7939 (m) REVERT: C 410 LYS cc_start: 0.7261 (pttt) cc_final: 0.6019 (mmtt) REVERT: D 13 VAL cc_start: 0.8416 (t) cc_final: 0.8110 (p) REVERT: D 16 ASP cc_start: 0.8558 (t70) cc_final: 0.8299 (t0) REVERT: D 170 GLU cc_start: 0.3580 (OUTLIER) cc_final: 0.2502 (tp30) REVERT: D 196 GLU cc_start: 0.7539 (mp0) cc_final: 0.7066 (mt-10) REVERT: D 203 ARG cc_start: 0.7663 (mpt90) cc_final: 0.6833 (mtp180) REVERT: D 217 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5796 (mm-30) REVERT: D 232 ASP cc_start: 0.8609 (m-30) cc_final: 0.8167 (m-30) REVERT: D 235 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6433 (pp) REVERT: D 261 ASP cc_start: 0.8267 (t0) cc_final: 0.7471 (m-30) REVERT: D 286 MET cc_start: 0.8768 (tpp) cc_final: 0.8242 (tpt) REVERT: D 351 SER cc_start: 0.8428 (t) cc_final: 0.8029 (m) REVERT: D 410 LYS cc_start: 0.7363 (pttt) cc_final: 0.5961 (mmtt) REVERT: E 15 ASP cc_start: 0.8510 (t0) cc_final: 0.8196 (t70) REVERT: E 105 ARG cc_start: 0.7292 (mtp-110) cc_final: 0.6722 (ttp80) REVERT: E 149 ARG cc_start: 0.6206 (mpt180) cc_final: 0.5692 (mpt180) REVERT: E 170 GLU cc_start: 0.3670 (OUTLIER) cc_final: 0.2391 (tp30) REVERT: E 196 GLU cc_start: 0.7665 (mp0) cc_final: 0.7201 (mt-10) REVERT: E 203 ARG cc_start: 0.7866 (mpt90) cc_final: 0.7086 (mtp180) REVERT: E 232 ASP cc_start: 0.8600 (m-30) cc_final: 0.8194 (m-30) REVERT: E 235 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.6699 (pp) REVERT: E 261 ASP cc_start: 0.8348 (t0) cc_final: 0.7628 (m-30) REVERT: E 286 MET cc_start: 0.8787 (tpp) cc_final: 0.8199 (tpt) REVERT: E 330 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8857 (pp) REVERT: E 351 SER cc_start: 0.8415 (t) cc_final: 0.8028 (m) REVERT: E 410 LYS cc_start: 0.7345 (pttt) cc_final: 0.6166 (mmtt) REVERT: E 509 TYR cc_start: 0.8068 (p90) cc_final: 0.7717 (p90) REVERT: F 13 VAL cc_start: 0.8447 (t) cc_final: 0.8137 (p) REVERT: F 149 ARG cc_start: 0.5955 (mpp-170) cc_final: 0.5672 (mpt180) REVERT: F 170 GLU cc_start: 0.3549 (OUTLIER) cc_final: 0.2327 (tp30) REVERT: F 196 GLU cc_start: 0.7505 (mp0) cc_final: 0.7021 (mt-10) REVERT: F 217 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.5864 (tp30) REVERT: F 232 ASP cc_start: 0.8559 (m-30) cc_final: 0.8185 (m-30) REVERT: F 235 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6440 (pp) REVERT: F 261 ASP cc_start: 0.8222 (t0) cc_final: 0.7462 (m-30) REVERT: F 286 MET cc_start: 0.8802 (tpp) cc_final: 0.8269 (tpt) REVERT: F 351 SER cc_start: 0.8382 (t) cc_final: 0.7997 (m) REVERT: F 410 LYS cc_start: 0.7349 (pttt) cc_final: 0.6021 (mmtt) REVERT: F 509 TYR cc_start: 0.8178 (p90) cc_final: 0.7585 (p90) REVERT: G 149 ARG cc_start: 0.6041 (mpt180) cc_final: 0.5585 (mpt180) REVERT: G 170 GLU cc_start: 0.3473 (OUTLIER) cc_final: 0.2300 (tp30) REVERT: G 196 GLU cc_start: 0.7584 (mp0) cc_final: 0.7113 (mt-10) REVERT: G 203 ARG cc_start: 0.7750 (mpt90) cc_final: 0.7029 (mtp180) REVERT: G 232 ASP cc_start: 0.8559 (m-30) cc_final: 0.8162 (m-30) REVERT: G 235 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.6695 (pp) REVERT: G 261 ASP cc_start: 0.8328 (t0) cc_final: 0.7575 (m-30) REVERT: G 286 MET cc_start: 0.8790 (tpp) cc_final: 0.8191 (tpt) REVERT: G 330 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8967 (pp) REVERT: G 351 SER cc_start: 0.8328 (t) cc_final: 0.7963 (m) REVERT: G 410 LYS cc_start: 0.7272 (pttt) cc_final: 0.6038 (mmtt) REVERT: G 509 TYR cc_start: 0.8119 (p90) cc_final: 0.7805 (p90) REVERT: H 105 ARG cc_start: 0.7224 (mtp-110) cc_final: 0.6686 (ttp80) REVERT: H 149 ARG cc_start: 0.5850 (mpp-170) cc_final: 0.5581 (mpt180) REVERT: H 170 GLU cc_start: 0.3513 (OUTLIER) cc_final: 0.2456 (tp30) REVERT: H 196 GLU cc_start: 0.7625 (mp0) cc_final: 0.7150 (mt-10) REVERT: H 217 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5764 (tp30) REVERT: H 235 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6429 (pp) REVERT: H 261 ASP cc_start: 0.8202 (t0) cc_final: 0.7388 (m-30) REVERT: H 286 MET cc_start: 0.8722 (tpp) cc_final: 0.8213 (tpt) REVERT: H 351 SER cc_start: 0.8397 (t) cc_final: 0.8007 (m) REVERT: H 410 LYS cc_start: 0.7469 (pttt) cc_final: 0.6088 (mmtt) REVERT: J 5 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8309 (mp) outliers start: 107 outliers final: 62 residues processed: 648 average time/residue: 0.1833 time to fit residues: 196.4245 Evaluate side-chains 596 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 508 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 485 SER Chi-restraints excluded: chain J residue 5 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 240 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 309 optimal weight: 3.9990 chunk 195 optimal weight: 0.8980 chunk 278 optimal weight: 0.9980 chunk 320 optimal weight: 0.0050 chunk 352 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN A 334 GLN B 334 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN D 334 GLN E 48 GLN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN F 334 GLN G 334 GLN ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.157569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121356 restraints weight = 36093.465| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.40 r_work: 0.3214 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31928 Z= 0.123 Angle : 0.544 6.337 43288 Z= 0.271 Chirality : 0.043 0.136 4928 Planarity : 0.004 0.040 5424 Dihedral : 16.953 178.135 4925 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.14 % Allowed : 12.07 % Favored : 83.79 % 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: -1.24 (0.13), residues: 3960 helix: 0.29 (0.15), residues: 1344 sheet: -1.24 (0.22), residues: 544 loop : -1.45 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 493 TYR 0.024 0.002 TYR C 110 PHE 0.009 0.001 PHE E 456 HIS 0.001 0.000 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00294 (31920) covalent geometry : angle 0.54416 (43288) hydrogen bonds : bond 0.02589 ( 1032) hydrogen bonds : angle 4.51944 ( 2952) Misc. bond : bond 0.00048 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 563 time to evaluate : 1.346 Fit side-chains REVERT: A 15 ASP cc_start: 0.8583 (t0) cc_final: 0.8235 (t70) REVERT: A 105 ARG cc_start: 0.7351 (mtp-110) cc_final: 0.6782 (ttp80) REVERT: A 170 GLU cc_start: 0.3938 (OUTLIER) cc_final: 0.2549 (tp30) REVERT: A 196 GLU cc_start: 0.7654 (mp0) cc_final: 0.7170 (mt-10) REVERT: A 203 ARG cc_start: 0.7832 (mpt90) cc_final: 0.6933 (mtm110) REVERT: A 232 ASP cc_start: 0.8597 (m-30) cc_final: 0.8159 (m-30) REVERT: A 235 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.6850 (pp) REVERT: A 286 MET cc_start: 0.8806 (tpp) cc_final: 0.8289 (tpt) REVERT: A 330 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.9033 (pp) REVERT: A 351 SER cc_start: 0.8446 (t) cc_final: 0.7982 (m) REVERT: A 408 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6566 (pp) REVERT: A 410 LYS cc_start: 0.7306 (pttt) cc_final: 0.6087 (mmtt) REVERT: A 509 TYR cc_start: 0.8091 (p90) cc_final: 0.7744 (p90) REVERT: B 13 VAL cc_start: 0.8501 (t) cc_final: 0.8234 (p) REVERT: B 15 ASP cc_start: 0.8621 (t0) cc_final: 0.8200 (t70) REVERT: B 105 ARG cc_start: 0.7381 (mtp-110) cc_final: 0.6844 (ttp80) REVERT: B 149 ARG cc_start: 0.6181 (mpt180) cc_final: 0.5581 (mpt180) REVERT: B 170 GLU cc_start: 0.3828 (OUTLIER) cc_final: 0.2481 (tp30) REVERT: B 196 GLU cc_start: 0.7621 (mp0) cc_final: 0.7126 (mt-10) REVERT: B 217 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5885 (mm-30) REVERT: B 232 ASP cc_start: 0.8543 (m-30) cc_final: 0.8150 (m-30) REVERT: B 235 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.6640 (pp) REVERT: B 286 MET cc_start: 0.8805 (tpp) cc_final: 0.8312 (tpt) REVERT: B 351 SER cc_start: 0.8544 (t) cc_final: 0.8088 (m) REVERT: B 410 LYS cc_start: 0.7346 (pttt) cc_final: 0.5989 (mmtt) REVERT: B 412 ARG cc_start: 0.8276 (ptp90) cc_final: 0.7919 (ptp90) REVERT: C 13 VAL cc_start: 0.8618 (t) cc_final: 0.8344 (p) REVERT: C 105 ARG cc_start: 0.7404 (mtp-110) cc_final: 0.6826 (ttp80) REVERT: C 170 GLU cc_start: 0.3652 (OUTLIER) cc_final: 0.2283 (tp30) REVERT: C 196 GLU cc_start: 0.7597 (mp0) cc_final: 0.7113 (mt-10) REVERT: C 203 ARG cc_start: 0.7789 (mpt90) cc_final: 0.6892 (mtm110) REVERT: C 232 ASP cc_start: 0.8554 (m-30) cc_final: 0.8101 (m-30) REVERT: C 235 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.6836 (pp) REVERT: C 286 MET cc_start: 0.8841 (tpp) cc_final: 0.8301 (tpt) REVERT: C 351 SER cc_start: 0.8486 (t) cc_final: 0.8028 (m) REVERT: C 410 LYS cc_start: 0.7292 (pttt) cc_final: 0.6027 (mmtt) REVERT: C 509 TYR cc_start: 0.8097 (p90) cc_final: 0.7752 (p90) REVERT: D 13 VAL cc_start: 0.8510 (t) cc_final: 0.8233 (p) REVERT: D 16 ASP cc_start: 0.8671 (t70) cc_final: 0.8403 (t0) REVERT: D 70 MET cc_start: 0.9194 (mtp) cc_final: 0.8955 (mtm) REVERT: D 149 ARG cc_start: 0.6232 (mpt180) cc_final: 0.5609 (mpt180) REVERT: D 170 GLU cc_start: 0.3736 (OUTLIER) cc_final: 0.2487 (tp30) REVERT: D 196 GLU cc_start: 0.7564 (mp0) cc_final: 0.7046 (mt-10) REVERT: D 217 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5859 (mm-30) REVERT: D 232 ASP cc_start: 0.8518 (m-30) cc_final: 0.8119 (m-30) REVERT: D 235 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.6596 (pp) REVERT: D 286 MET cc_start: 0.8810 (tpp) cc_final: 0.8354 (tpt) REVERT: D 327 SER cc_start: 0.8928 (p) cc_final: 0.8617 (t) REVERT: D 351 SER cc_start: 0.8534 (t) cc_final: 0.8095 (m) REVERT: D 410 LYS cc_start: 0.7398 (pttt) cc_final: 0.5983 (mmtt) REVERT: D 509 TYR cc_start: 0.8090 (p90) cc_final: 0.7762 (p90) REVERT: E 15 ASP cc_start: 0.8547 (t0) cc_final: 0.8232 (t70) REVERT: E 105 ARG cc_start: 0.7310 (mtp-110) cc_final: 0.6709 (ttp80) REVERT: E 170 GLU cc_start: 0.3777 (OUTLIER) cc_final: 0.2379 (tp30) REVERT: E 196 GLU cc_start: 0.7745 (mp0) cc_final: 0.7260 (mt-10) REVERT: E 203 ARG cc_start: 0.7939 (mpt90) cc_final: 0.7068 (mtm110) REVERT: E 232 ASP cc_start: 0.8571 (m-30) cc_final: 0.8142 (m-30) REVERT: E 235 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.6816 (pp) REVERT: E 286 MET cc_start: 0.8857 (tpp) cc_final: 0.8327 (tpt) REVERT: E 330 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8934 (pp) REVERT: E 351 SER cc_start: 0.8520 (t) cc_final: 0.8078 (m) REVERT: E 410 LYS cc_start: 0.7273 (pttt) cc_final: 0.6075 (mmtt) REVERT: E 509 TYR cc_start: 0.8034 (p90) cc_final: 0.7668 (p90) REVERT: F 13 VAL cc_start: 0.8533 (t) cc_final: 0.8249 (p) REVERT: F 15 ASP cc_start: 0.8640 (t0) cc_final: 0.8206 (t70) REVERT: F 170 GLU cc_start: 0.3584 (OUTLIER) cc_final: 0.2310 (tp30) REVERT: F 196 GLU cc_start: 0.7618 (mp0) cc_final: 0.7108 (mt-10) REVERT: F 217 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.5872 (mm-30) REVERT: F 232 ASP cc_start: 0.8533 (m-30) cc_final: 0.8124 (m-30) REVERT: F 235 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.6609 (pp) REVERT: F 351 SER cc_start: 0.8530 (t) cc_final: 0.8078 (m) REVERT: F 410 LYS cc_start: 0.7403 (pttt) cc_final: 0.6048 (mmtt) REVERT: G 15 ASP cc_start: 0.8619 (t0) cc_final: 0.8266 (t70) REVERT: G 170 GLU cc_start: 0.3557 (OUTLIER) cc_final: 0.2164 (tp30) REVERT: G 196 GLU cc_start: 0.7673 (mp0) cc_final: 0.7169 (mt-10) REVERT: G 203 ARG cc_start: 0.7836 (mpt90) cc_final: 0.6942 (mtm110) REVERT: G 232 ASP cc_start: 0.8538 (m-30) cc_final: 0.8095 (m-30) REVERT: G 235 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.6831 (pp) REVERT: G 286 MET cc_start: 0.8809 (tpp) cc_final: 0.8321 (tpt) REVERT: G 330 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.9032 (pp) REVERT: G 351 SER cc_start: 0.8451 (t) cc_final: 0.8020 (m) REVERT: G 408 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6540 (pp) REVERT: G 410 LYS cc_start: 0.7313 (pttt) cc_final: 0.6080 (mmtt) REVERT: H 13 VAL cc_start: 0.8523 (t) cc_final: 0.8267 (p) REVERT: H 15 ASP cc_start: 0.8629 (t0) cc_final: 0.8159 (t70) REVERT: H 105 ARG cc_start: 0.7278 (mtp-110) cc_final: 0.6697 (ttp80) REVERT: H 149 ARG cc_start: 0.5978 (mpp-170) cc_final: 0.5777 (mpt180) REVERT: H 170 GLU cc_start: 0.3897 (OUTLIER) cc_final: 0.2539 (tp30) REVERT: H 196 GLU cc_start: 0.7716 (mp0) cc_final: 0.7227 (mt-10) REVERT: H 199 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7470 (mt-10) REVERT: H 217 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5692 (tp30) REVERT: H 235 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.6540 (pp) REVERT: H 286 MET cc_start: 0.8764 (tpp) cc_final: 0.8322 (tpt) REVERT: H 327 SER cc_start: 0.8943 (p) cc_final: 0.8662 (t) REVERT: H 351 SER cc_start: 0.8524 (t) cc_final: 0.8071 (m) REVERT: H 410 LYS cc_start: 0.7469 (pttt) cc_final: 0.6120 (mmtt) REVERT: H 509 TYR cc_start: 0.8127 (p90) cc_final: 0.7834 (p90) outliers start: 135 outliers final: 75 residues processed: 666 average time/residue: 0.1768 time to fit residues: 194.9064 Evaluate side-chains 623 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 523 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 485 SER Chi-restraints excluded: chain I residue 7 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 139 optimal weight: 0.6980 chunk 187 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 chunk 375 optimal weight: 4.9990 chunk 386 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 232 optimal weight: 0.0170 chunk 382 optimal weight: 3.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 334 GLN A 498 GLN B 309 GLN B 334 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN D 334 GLN E 48 GLN E 309 GLN E 334 GLN F 309 GLN F 334 GLN G 48 GLN G 309 GLN G 334 GLN H 309 GLN H 334 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.158103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.121948 restraints weight = 36241.492| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.40 r_work: 0.3220 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31928 Z= 0.111 Angle : 0.531 6.272 43288 Z= 0.263 Chirality : 0.043 0.132 4928 Planarity : 0.004 0.038 5424 Dihedral : 16.665 175.998 4924 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.17 % Allowed : 13.45 % Favored : 82.38 % 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: -0.92 (0.13), residues: 3960 helix: 0.65 (0.15), residues: 1336 sheet: -1.14 (0.22), residues: 544 loop : -1.31 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 493 TYR 0.026 0.002 TYR H 110 PHE 0.006 0.001 PHE E 456 HIS 0.001 0.000 HIS G 504 Details of bonding type rmsd covalent geometry : bond 0.00261 (31920) covalent geometry : angle 0.53050 (43288) hydrogen bonds : bond 0.02476 ( 1032) hydrogen bonds : angle 4.37482 ( 2952) Misc. bond : bond 0.00035 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 543 time to evaluate : 1.128 Fit side-chains REVERT: A 105 ARG cc_start: 0.7385 (mtp-110) cc_final: 0.6807 (ttp80) REVERT: A 170 GLU cc_start: 0.3913 (OUTLIER) cc_final: 0.2604 (tp30) REVERT: A 196 GLU cc_start: 0.7656 (mp0) cc_final: 0.7159 (mt-10) REVERT: A 199 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7404 (mt-10) REVERT: A 232 ASP cc_start: 0.8610 (m-30) cc_final: 0.8191 (m-30) REVERT: A 235 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.6800 (pp) REVERT: A 330 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8995 (pp) REVERT: A 351 SER cc_start: 0.8504 (t) cc_final: 0.8003 (m) REVERT: A 408 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6507 (pp) REVERT: A 410 LYS cc_start: 0.7339 (pttt) cc_final: 0.6041 (mmtt) REVERT: B 15 ASP cc_start: 0.8626 (t0) cc_final: 0.8215 (t70) REVERT: B 105 ARG cc_start: 0.7381 (mtp-110) cc_final: 0.6817 (ttp80) REVERT: B 170 GLU cc_start: 0.3786 (OUTLIER) cc_final: 0.2485 (tp30) REVERT: B 196 GLU cc_start: 0.7731 (mp0) cc_final: 0.7225 (mt-10) REVERT: B 217 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.5854 (mm-30) REVERT: B 232 ASP cc_start: 0.8585 (m-30) cc_final: 0.8165 (m-30) REVERT: B 235 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.6577 (pp) REVERT: B 351 SER cc_start: 0.8557 (t) cc_final: 0.8075 (m) REVERT: B 408 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6648 (pp) REVERT: B 410 LYS cc_start: 0.7365 (pttt) cc_final: 0.5977 (mmtt) REVERT: C 105 ARG cc_start: 0.7423 (mtp-110) cc_final: 0.6847 (ttp80) REVERT: C 170 GLU cc_start: 0.3727 (OUTLIER) cc_final: 0.2423 (tp30) REVERT: C 196 GLU cc_start: 0.7611 (mp0) cc_final: 0.7112 (mt-10) REVERT: C 203 ARG cc_start: 0.7800 (mpt90) cc_final: 0.6880 (mtm110) REVERT: C 217 GLU cc_start: 0.5938 (tp30) cc_final: 0.5600 (tp30) REVERT: C 228 LYS cc_start: 0.7739 (tttp) cc_final: 0.7339 (tttp) REVERT: C 232 ASP cc_start: 0.8515 (m-30) cc_final: 0.8071 (m-30) REVERT: C 235 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.6745 (pp) REVERT: C 286 MET cc_start: 0.8832 (tpp) cc_final: 0.8339 (tpt) REVERT: C 351 SER cc_start: 0.8515 (t) cc_final: 0.8041 (m) REVERT: C 408 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6509 (pp) REVERT: C 410 LYS cc_start: 0.7306 (pttt) cc_final: 0.6062 (mmtt) REVERT: D 13 VAL cc_start: 0.8525 (t) cc_final: 0.8206 (p) REVERT: D 16 ASP cc_start: 0.8710 (t70) cc_final: 0.8424 (t0) REVERT: D 170 GLU cc_start: 0.3582 (OUTLIER) cc_final: 0.2410 (tp30) REVERT: D 196 GLU cc_start: 0.7652 (mp0) cc_final: 0.7130 (mt-10) REVERT: D 217 GLU cc_start: 0.6277 (OUTLIER) cc_final: 0.5755 (tp30) REVERT: D 232 ASP cc_start: 0.8545 (m-30) cc_final: 0.8107 (m-30) REVERT: D 235 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6525 (pp) REVERT: D 351 SER cc_start: 0.8543 (t) cc_final: 0.8071 (m) REVERT: D 399 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6423 (mm-30) REVERT: D 408 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6624 (pp) REVERT: D 410 LYS cc_start: 0.7389 (pttt) cc_final: 0.5990 (mmtt) REVERT: E 105 ARG cc_start: 0.7338 (mtp-110) cc_final: 0.6742 (ttp80) REVERT: E 170 GLU cc_start: 0.3683 (OUTLIER) cc_final: 0.2280 (tp30) REVERT: E 196 GLU cc_start: 0.7761 (mp0) cc_final: 0.7264 (mt-10) REVERT: E 203 ARG cc_start: 0.7934 (mpt90) cc_final: 0.7030 (mtm110) REVERT: E 232 ASP cc_start: 0.8580 (m-30) cc_final: 0.8143 (m-30) REVERT: E 235 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.6824 (pp) REVERT: E 286 MET cc_start: 0.8826 (tpp) cc_final: 0.8358 (tpt) REVERT: E 330 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8966 (pp) REVERT: E 351 SER cc_start: 0.8537 (t) cc_final: 0.8054 (m) REVERT: E 408 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6482 (pp) REVERT: E 410 LYS cc_start: 0.7255 (pttt) cc_final: 0.6087 (mmtt) REVERT: F 15 ASP cc_start: 0.8614 (t0) cc_final: 0.8180 (t70) REVERT: F 149 ARG cc_start: 0.6107 (mpt180) cc_final: 0.5667 (mpt180) REVERT: F 170 GLU cc_start: 0.3628 (OUTLIER) cc_final: 0.2336 (tp30) REVERT: F 196 GLU cc_start: 0.7735 (mp0) cc_final: 0.7216 (mt-10) REVERT: F 217 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5810 (mm-30) REVERT: F 228 LYS cc_start: 0.7691 (tttp) cc_final: 0.7283 (tttp) REVERT: F 232 ASP cc_start: 0.8535 (m-30) cc_final: 0.8125 (m-30) REVERT: F 235 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6540 (pp) REVERT: F 351 SER cc_start: 0.8545 (t) cc_final: 0.8071 (m) REVERT: F 399 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6364 (mm-30) REVERT: F 408 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6630 (pp) REVERT: F 410 LYS cc_start: 0.7390 (pttt) cc_final: 0.6027 (mmtt) REVERT: G 170 GLU cc_start: 0.3470 (OUTLIER) cc_final: 0.2246 (tp30) REVERT: G 196 GLU cc_start: 0.7677 (mp0) cc_final: 0.7154 (mt-10) REVERT: G 203 ARG cc_start: 0.7830 (mpt90) cc_final: 0.6926 (mtm110) REVERT: G 232 ASP cc_start: 0.8534 (m-30) cc_final: 0.8095 (m-30) REVERT: G 235 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.6732 (pp) REVERT: G 286 MET cc_start: 0.8842 (tpp) cc_final: 0.8385 (tpt) REVERT: G 330 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9047 (pp) REVERT: G 351 SER cc_start: 0.8493 (t) cc_final: 0.8023 (m) REVERT: G 408 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6477 (pp) REVERT: G 410 LYS cc_start: 0.7288 (pttt) cc_final: 0.6071 (mmtt) REVERT: H 15 ASP cc_start: 0.8618 (t0) cc_final: 0.8196 (t70) REVERT: H 105 ARG cc_start: 0.7273 (mtp-110) cc_final: 0.6679 (ttp80) REVERT: H 170 GLU cc_start: 0.3879 (OUTLIER) cc_final: 0.2541 (tp30) REVERT: H 196 GLU cc_start: 0.7811 (mp0) cc_final: 0.7296 (mt-10) REVERT: H 199 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7483 (mt-10) REVERT: H 217 GLU cc_start: 0.6173 (OUTLIER) cc_final: 0.5783 (tp30) REVERT: H 235 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6521 (pp) REVERT: H 286 MET cc_start: 0.8795 (tpp) cc_final: 0.8386 (tpt) REVERT: H 351 SER cc_start: 0.8560 (t) cc_final: 0.8058 (m) REVERT: H 408 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6598 (pp) REVERT: H 410 LYS cc_start: 0.7469 (pttt) cc_final: 0.6133 (mmtt) REVERT: H 509 TYR cc_start: 0.8073 (p90) cc_final: 0.7777 (p90) outliers start: 136 outliers final: 76 residues processed: 650 average time/residue: 0.1884 time to fit residues: 201.3997 Evaluate side-chains 631 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 522 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 336 optimal weight: 3.9990 chunk 341 optimal weight: 4.9990 chunk 288 optimal weight: 6.9990 chunk 339 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 279 optimal weight: 2.9990 chunk 297 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 HIS B 48 GLN C 48 GLN C 112 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 466 HIS D 48 GLN D 334 GLN D 466 HIS E 112 GLN E 466 HIS F 309 GLN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 466 HIS G 498 GLN H 334 GLN H 466 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.152429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116305 restraints weight = 36394.657| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.35 r_work: 0.3145 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31928 Z= 0.184 Angle : 0.592 6.705 43288 Z= 0.296 Chirality : 0.045 0.147 4928 Planarity : 0.004 0.039 5424 Dihedral : 16.832 176.247 4924 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.38 % Allowed : 13.91 % Favored : 81.71 % 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: -0.85 (0.13), residues: 3960 helix: 0.67 (0.15), residues: 1328 sheet: -1.08 (0.23), residues: 504 loop : -1.24 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 493 TYR 0.023 0.002 TYR A 411 PHE 0.007 0.001 PHE H 24 HIS 0.001 0.000 HIS E 504 Details of bonding type rmsd covalent geometry : bond 0.00451 (31920) covalent geometry : angle 0.59226 (43288) hydrogen bonds : bond 0.03118 ( 1032) hydrogen bonds : angle 4.50176 ( 2952) Misc. bond : bond 0.00084 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 546 time to evaluate : 1.232 Fit side-chains REVERT: A 105 ARG cc_start: 0.7497 (mtp-110) cc_final: 0.6823 (ttp80) REVERT: A 170 GLU cc_start: 0.3849 (OUTLIER) cc_final: 0.2422 (tp30) REVERT: A 196 GLU cc_start: 0.7745 (mp0) cc_final: 0.7280 (mt-10) REVERT: A 232 ASP cc_start: 0.8499 (m-30) cc_final: 0.8124 (m-30) REVERT: A 235 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.6803 (pp) REVERT: A 286 MET cc_start: 0.8799 (tpp) cc_final: 0.8375 (tpt) REVERT: A 330 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9027 (pp) REVERT: A 408 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6576 (pp) REVERT: A 410 LYS cc_start: 0.7419 (pttt) cc_final: 0.6061 (mmtt) REVERT: B 15 ASP cc_start: 0.8674 (t0) cc_final: 0.8284 (t70) REVERT: B 105 ARG cc_start: 0.7518 (mtp-110) cc_final: 0.6849 (ttp80) REVERT: B 112 GLN cc_start: 0.7455 (tp40) cc_final: 0.7242 (tp-100) REVERT: B 126 ARG cc_start: 0.5094 (mpt90) cc_final: 0.2200 (mtp180) REVERT: B 196 GLU cc_start: 0.7730 (mp0) cc_final: 0.7211 (mt-10) REVERT: B 217 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5798 (tp30) REVERT: B 232 ASP cc_start: 0.8405 (m-30) cc_final: 0.8013 (m-30) REVERT: B 235 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.6604 (pp) REVERT: B 286 MET cc_start: 0.8810 (tpp) cc_final: 0.8403 (tpt) REVERT: B 408 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6687 (pp) REVERT: B 410 LYS cc_start: 0.7419 (pttt) cc_final: 0.5948 (mmtt) REVERT: C 105 ARG cc_start: 0.7531 (mtp-110) cc_final: 0.6849 (ttp80) REVERT: C 170 GLU cc_start: 0.3709 (OUTLIER) cc_final: 0.2207 (tp30) REVERT: C 196 GLU cc_start: 0.7538 (mp0) cc_final: 0.7108 (mt-10) REVERT: C 203 ARG cc_start: 0.7944 (mpt90) cc_final: 0.7107 (mtm110) REVERT: C 228 LYS cc_start: 0.7746 (tttp) cc_final: 0.7419 (tttp) REVERT: C 232 ASP cc_start: 0.8319 (m-30) cc_final: 0.7879 (m-30) REVERT: C 235 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.6818 (pp) REVERT: C 286 MET cc_start: 0.8842 (tpp) cc_final: 0.8397 (tpt) REVERT: C 330 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9018 (pp) REVERT: C 408 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6576 (pp) REVERT: C 410 LYS cc_start: 0.7386 (pttt) cc_final: 0.5994 (mmtt) REVERT: D 13 VAL cc_start: 0.8675 (t) cc_final: 0.8401 (p) REVERT: D 15 ASP cc_start: 0.8680 (t0) cc_final: 0.8281 (t70) REVERT: D 112 GLN cc_start: 0.7446 (tp40) cc_final: 0.7245 (tp-100) REVERT: D 126 ARG cc_start: 0.5076 (mpt90) cc_final: 0.2147 (mtp180) REVERT: D 196 GLU cc_start: 0.7653 (mp0) cc_final: 0.7138 (mt-10) REVERT: D 217 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5922 (mm-30) REVERT: D 232 ASP cc_start: 0.8355 (m-30) cc_final: 0.7954 (m-30) REVERT: D 235 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6554 (pp) REVERT: D 286 MET cc_start: 0.8814 (tpp) cc_final: 0.8374 (tpt) REVERT: D 408 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6722 (pp) REVERT: D 410 LYS cc_start: 0.7454 (pttt) cc_final: 0.5973 (mmtt) REVERT: E 105 ARG cc_start: 0.7461 (mtp-110) cc_final: 0.6787 (ttp80) REVERT: E 170 GLU cc_start: 0.3659 (OUTLIER) cc_final: 0.2148 (tp30) REVERT: E 196 GLU cc_start: 0.7715 (mp0) cc_final: 0.7278 (mt-10) REVERT: E 203 ARG cc_start: 0.7929 (mpt90) cc_final: 0.7133 (mtm110) REVERT: E 232 ASP cc_start: 0.8394 (m-30) cc_final: 0.7969 (m-30) REVERT: E 235 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.6867 (pp) REVERT: E 286 MET cc_start: 0.8857 (tpp) cc_final: 0.8419 (tpt) REVERT: E 330 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8989 (pp) REVERT: E 408 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6554 (pp) REVERT: E 410 LYS cc_start: 0.7343 (pttt) cc_final: 0.6025 (mmtt) REVERT: F 15 ASP cc_start: 0.8707 (t0) cc_final: 0.8320 (t70) REVERT: F 112 GLN cc_start: 0.7451 (tp40) cc_final: 0.7239 (tp-100) REVERT: F 126 ARG cc_start: 0.5069 (mpt90) cc_final: 0.2174 (mtp180) REVERT: F 196 GLU cc_start: 0.7752 (mp0) cc_final: 0.7214 (mt-10) REVERT: F 217 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.5863 (tp30) REVERT: F 232 ASP cc_start: 0.8366 (m-30) cc_final: 0.7979 (m-30) REVERT: F 235 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.6591 (pp) REVERT: F 408 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6642 (pp) REVERT: F 410 LYS cc_start: 0.7417 (pttt) cc_final: 0.5984 (mmtt) REVERT: G 170 GLU cc_start: 0.3484 (OUTLIER) cc_final: 0.2131 (tp30) REVERT: G 196 GLU cc_start: 0.7638 (mp0) cc_final: 0.7185 (mt-10) REVERT: G 203 ARG cc_start: 0.7974 (mpt90) cc_final: 0.7139 (mtm110) REVERT: G 232 ASP cc_start: 0.8348 (m-30) cc_final: 0.7962 (m-30) REVERT: G 235 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6744 (pp) REVERT: G 286 MET cc_start: 0.8851 (tpp) cc_final: 0.8424 (tpt) REVERT: G 330 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.9091 (pp) REVERT: G 408 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6580 (pp) REVERT: G 410 LYS cc_start: 0.7530 (pttt) cc_final: 0.6243 (mmtt) REVERT: H 105 ARG cc_start: 0.7428 (mtp-110) cc_final: 0.6746 (ttp80) REVERT: H 170 GLU cc_start: 0.3723 (OUTLIER) cc_final: 0.2337 (tp30) REVERT: H 196 GLU cc_start: 0.7820 (mp0) cc_final: 0.7299 (mt-10) REVERT: H 217 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5819 (tp30) REVERT: H 235 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6578 (pp) REVERT: H 286 MET cc_start: 0.8788 (tpp) cc_final: 0.8405 (tpt) REVERT: H 408 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6607 (pp) REVERT: H 410 LYS cc_start: 0.7434 (pttt) cc_final: 0.5980 (mmtt) outliers start: 143 outliers final: 84 residues processed: 654 average time/residue: 0.1902 time to fit residues: 205.4863 Evaluate side-chains 629 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 516 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 331 CYS Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain I residue 7 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 168 optimal weight: 0.9980 chunk 296 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 271 optimal weight: 0.2980 chunk 360 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 264 optimal weight: 0.7980 chunk 335 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 334 GLN B 48 GLN B 334 GLN C 48 GLN C 112 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN D 48 GLN D 334 GLN E 112 GLN E 334 GLN G 48 GLN G 112 GLN G 334 GLN H 112 GLN H 334 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.155968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.119776 restraints weight = 36415.748| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.37 r_work: 0.3194 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31928 Z= 0.116 Angle : 0.545 6.259 43288 Z= 0.272 Chirality : 0.043 0.134 4928 Planarity : 0.004 0.040 5424 Dihedral : 16.483 175.760 4912 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.43 % Allowed : 15.38 % Favored : 81.19 % 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: -0.70 (0.14), residues: 3960 helix: 0.85 (0.15), residues: 1336 sheet: -1.08 (0.22), residues: 544 loop : -1.17 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 493 TYR 0.017 0.001 TYR E 509 PHE 0.012 0.001 PHE D 401 HIS 0.002 0.000 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00273 (31920) covalent geometry : angle 0.54453 (43288) hydrogen bonds : bond 0.02537 ( 1032) hydrogen bonds : angle 4.38373 ( 2952) Misc. bond : bond 0.00025 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 520 time to evaluate : 1.091 Fit side-chains REVERT: A 105 ARG cc_start: 0.7430 (mtp-110) cc_final: 0.6749 (ttp80) REVERT: A 170 GLU cc_start: 0.3845 (OUTLIER) cc_final: 0.2689 (tp30) REVERT: A 196 GLU cc_start: 0.7607 (mp0) cc_final: 0.7159 (mt-10) REVERT: A 199 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7236 (mt-10) REVERT: A 232 ASP cc_start: 0.8399 (m-30) cc_final: 0.8190 (m-30) REVERT: A 235 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6906 (pp) REVERT: A 330 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8992 (pp) REVERT: A 408 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6416 (pp) REVERT: A 410 LYS cc_start: 0.7426 (pttt) cc_final: 0.6025 (mmtt) REVERT: B 105 ARG cc_start: 0.7427 (mtp-110) cc_final: 0.6769 (ttp80) REVERT: B 126 ARG cc_start: 0.5036 (mpt90) cc_final: 0.2183 (mtp180) REVERT: B 196 GLU cc_start: 0.7733 (mp0) cc_final: 0.7226 (mt-10) REVERT: B 199 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7401 (mt-10) REVERT: B 217 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5591 (tp30) REVERT: B 232 ASP cc_start: 0.8381 (m-30) cc_final: 0.8177 (m-30) REVERT: B 235 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6534 (pp) REVERT: B 319 ASP cc_start: 0.8310 (m-30) cc_final: 0.8004 (m-30) REVERT: B 408 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6562 (pp) REVERT: B 410 LYS cc_start: 0.7405 (pttt) cc_final: 0.5910 (mmtt) REVERT: C 105 ARG cc_start: 0.7435 (mtp-110) cc_final: 0.6767 (ttp80) REVERT: C 170 GLU cc_start: 0.3847 (OUTLIER) cc_final: 0.2574 (tp30) REVERT: C 196 GLU cc_start: 0.7550 (mp0) cc_final: 0.7055 (mt-10) REVERT: C 203 ARG cc_start: 0.7850 (mpt90) cc_final: 0.6976 (mtm110) REVERT: C 235 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.6778 (pp) REVERT: C 286 MET cc_start: 0.8781 (tpp) cc_final: 0.8381 (tpt) REVERT: C 330 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.9013 (pp) REVERT: C 408 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6484 (pp) REVERT: C 410 LYS cc_start: 0.7335 (pttt) cc_final: 0.5980 (mmtt) REVERT: D 13 VAL cc_start: 0.8639 (t) cc_final: 0.8338 (p) REVERT: D 15 ASP cc_start: 0.8692 (t0) cc_final: 0.8272 (t70) REVERT: D 126 ARG cc_start: 0.5025 (mpt90) cc_final: 0.2173 (mtp180) REVERT: D 196 GLU cc_start: 0.7682 (mp0) cc_final: 0.7149 (mt-10) REVERT: D 217 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5697 (tp30) REVERT: D 228 LYS cc_start: 0.7724 (tttp) cc_final: 0.7445 (tttp) REVERT: D 232 ASP cc_start: 0.8361 (m-30) cc_final: 0.7985 (m-30) REVERT: D 235 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6705 (pp) REVERT: D 319 ASP cc_start: 0.8294 (m-30) cc_final: 0.8062 (m-30) REVERT: D 330 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.9030 (pp) REVERT: D 408 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6687 (pp) REVERT: D 410 LYS cc_start: 0.7408 (pttt) cc_final: 0.5894 (mmtt) REVERT: E 105 ARG cc_start: 0.7396 (mtp-110) cc_final: 0.6698 (ttp80) REVERT: E 170 GLU cc_start: 0.3763 (OUTLIER) cc_final: 0.2505 (tp30) REVERT: E 196 GLU cc_start: 0.7682 (mp0) cc_final: 0.7221 (mt-10) REVERT: E 199 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7296 (mt-10) REVERT: E 203 ARG cc_start: 0.7928 (mpt90) cc_final: 0.7076 (mtm110) REVERT: E 235 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.6744 (pp) REVERT: E 286 MET cc_start: 0.8800 (tpp) cc_final: 0.8411 (tpt) REVERT: E 330 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8931 (pp) REVERT: E 408 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6393 (pp) REVERT: E 410 LYS cc_start: 0.7300 (pttt) cc_final: 0.6012 (mmtt) REVERT: F 126 ARG cc_start: 0.5081 (mpt90) cc_final: 0.2229 (mtp180) REVERT: F 149 ARG cc_start: 0.6341 (mpt180) cc_final: 0.5905 (mpt180) REVERT: F 196 GLU cc_start: 0.7733 (mp0) cc_final: 0.7216 (mt-10) REVERT: F 217 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.5797 (tp30) REVERT: F 235 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6736 (pp) REVERT: F 408 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6578 (pp) REVERT: F 410 LYS cc_start: 0.7369 (pttt) cc_final: 0.5976 (mmtt) REVERT: G 170 GLU cc_start: 0.3552 (OUTLIER) cc_final: 0.2412 (tp30) REVERT: G 196 GLU cc_start: 0.7634 (mp0) cc_final: 0.7128 (mt-10) REVERT: G 199 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7387 (mt-10) REVERT: G 232 ASP cc_start: 0.8321 (m-30) cc_final: 0.8099 (m-30) REVERT: G 235 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6831 (pp) REVERT: G 330 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.9027 (pp) REVERT: G 408 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6452 (pp) REVERT: G 410 LYS cc_start: 0.7396 (pttt) cc_final: 0.6072 (mmtt) REVERT: G 459 TYR cc_start: 0.8745 (t80) cc_final: 0.8462 (t80) REVERT: H 105 ARG cc_start: 0.7349 (mtp-110) cc_final: 0.6663 (ttp80) REVERT: H 170 GLU cc_start: 0.3753 (OUTLIER) cc_final: 0.2665 (tp30) REVERT: H 196 GLU cc_start: 0.7802 (mp0) cc_final: 0.7294 (mt-10) REVERT: H 199 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7472 (mt-10) REVERT: H 217 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5870 (tp30) REVERT: H 235 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6512 (pp) REVERT: H 286 MET cc_start: 0.8755 (tpp) cc_final: 0.8394 (tpt) REVERT: H 330 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8934 (pp) REVERT: H 408 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6484 (pp) REVERT: H 410 LYS cc_start: 0.7332 (pttt) cc_final: 0.5933 (mmtt) outliers start: 112 outliers final: 66 residues processed: 603 average time/residue: 0.1960 time to fit residues: 193.0314 Evaluate side-chains 594 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 497 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 357 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 387 optimal weight: 0.0970 chunk 349 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 48 GLN B 112 GLN C 48 GLN C 112 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN D 112 GLN D 334 GLN E 112 GLN F 48 GLN F 112 GLN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN G 112 GLN H 48 GLN H 112 GLN H 277 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.158050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121359 restraints weight = 36271.635| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.38 r_work: 0.3190 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31928 Z= 0.120 Angle : 0.549 6.264 43288 Z= 0.274 Chirality : 0.043 0.134 4928 Planarity : 0.004 0.040 5424 Dihedral : 16.356 175.143 4912 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.55 % Allowed : 14.98 % Favored : 81.46 % 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: -0.58 (0.14), residues: 3960 helix: 0.96 (0.15), residues: 1336 sheet: -1.02 (0.22), residues: 544 loop : -1.10 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 493 TYR 0.016 0.001 TYR C 509 PHE 0.011 0.001 PHE D 401 HIS 0.001 0.000 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00287 (31920) covalent geometry : angle 0.54910 (43288) hydrogen bonds : bond 0.02555 ( 1032) hydrogen bonds : angle 4.33841 ( 2952) Misc. bond : bond 0.00038 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 515 time to evaluate : 1.086 Fit side-chains REVERT: A 105 ARG cc_start: 0.7516 (mtp-110) cc_final: 0.6818 (ttp80) REVERT: A 170 GLU cc_start: 0.3861 (OUTLIER) cc_final: 0.2729 (tp30) REVERT: A 196 GLU cc_start: 0.7650 (mp0) cc_final: 0.7203 (mt-10) REVERT: A 199 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7258 (mt-10) REVERT: A 232 ASP cc_start: 0.8413 (m-30) cc_final: 0.8197 (m-30) REVERT: A 235 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6994 (pp) REVERT: A 330 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9041 (pp) REVERT: A 408 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6498 (pp) REVERT: A 410 LYS cc_start: 0.7477 (pttt) cc_final: 0.6081 (mmtt) REVERT: B 105 ARG cc_start: 0.7525 (mtp-110) cc_final: 0.6833 (ttp80) REVERT: B 126 ARG cc_start: 0.5061 (mpt90) cc_final: 0.2375 (mmm-85) REVERT: B 196 GLU cc_start: 0.7738 (mp0) cc_final: 0.7245 (mt-10) REVERT: B 199 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7409 (mt-10) REVERT: B 217 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5692 (tp30) REVERT: B 232 ASP cc_start: 0.8397 (m-30) cc_final: 0.8084 (m-30) REVERT: B 235 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6819 (pp) REVERT: B 319 ASP cc_start: 0.8226 (m-30) cc_final: 0.7927 (m-30) REVERT: B 330 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.9012 (pp) REVERT: B 408 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6615 (pp) REVERT: B 410 LYS cc_start: 0.7473 (pttt) cc_final: 0.5994 (mmtt) REVERT: C 105 ARG cc_start: 0.7531 (mtp-110) cc_final: 0.6829 (ttp80) REVERT: C 170 GLU cc_start: 0.3864 (OUTLIER) cc_final: 0.2602 (tp30) REVERT: C 196 GLU cc_start: 0.7578 (mp0) cc_final: 0.7079 (mt-10) REVERT: C 199 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7336 (mt-10) REVERT: C 232 ASP cc_start: 0.8376 (m-30) cc_final: 0.8174 (m-30) REVERT: C 235 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.6958 (pp) REVERT: C 330 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9049 (pp) REVERT: C 408 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6523 (pp) REVERT: C 410 LYS cc_start: 0.7371 (pttt) cc_final: 0.6039 (mmtt) REVERT: D 13 VAL cc_start: 0.8667 (t) cc_final: 0.8376 (p) REVERT: D 15 ASP cc_start: 0.8721 (t0) cc_final: 0.8420 (t70) REVERT: D 196 GLU cc_start: 0.7633 (mp0) cc_final: 0.7131 (mt-10) REVERT: D 217 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.5797 (tp30) REVERT: D 232 ASP cc_start: 0.8356 (m-30) cc_final: 0.8048 (m-30) REVERT: D 235 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6885 (pp) REVERT: D 330 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9075 (pp) REVERT: D 408 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6738 (pp) REVERT: D 410 LYS cc_start: 0.7462 (pttt) cc_final: 0.5950 (mmtt) REVERT: E 105 ARG cc_start: 0.7499 (mtp-110) cc_final: 0.6780 (ttp80) REVERT: E 170 GLU cc_start: 0.3727 (OUTLIER) cc_final: 0.2534 (tp30) REVERT: E 196 GLU cc_start: 0.7672 (mp0) cc_final: 0.7213 (mt-10) REVERT: E 199 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7319 (mt-10) REVERT: E 203 ARG cc_start: 0.7945 (mpt90) cc_final: 0.7096 (mtm110) REVERT: E 232 ASP cc_start: 0.8372 (m-30) cc_final: 0.8169 (m-30) REVERT: E 235 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6947 (pp) REVERT: E 286 MET cc_start: 0.8889 (tpp) cc_final: 0.8507 (tpt) REVERT: E 330 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8957 (pp) REVERT: E 408 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6478 (pp) REVERT: E 410 LYS cc_start: 0.7343 (pttt) cc_final: 0.6101 (mmtt) REVERT: E 459 TYR cc_start: 0.8786 (t80) cc_final: 0.8497 (t80) REVERT: F 126 ARG cc_start: 0.5106 (mpt90) cc_final: 0.2453 (mmm-85) REVERT: F 149 ARG cc_start: 0.6435 (mpt180) cc_final: 0.5968 (mpt180) REVERT: F 196 GLU cc_start: 0.7696 (mp0) cc_final: 0.7217 (mt-10) REVERT: F 199 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7435 (mt-10) REVERT: F 217 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5716 (tp30) REVERT: F 235 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6805 (pp) REVERT: F 408 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6640 (pp) REVERT: F 410 LYS cc_start: 0.7423 (pttt) cc_final: 0.6029 (mmtt) REVERT: G 170 GLU cc_start: 0.3502 (OUTLIER) cc_final: 0.2371 (tp30) REVERT: G 196 GLU cc_start: 0.7728 (mp0) cc_final: 0.7223 (mt-10) REVERT: G 199 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7337 (mt-10) REVERT: G 232 ASP cc_start: 0.8339 (m-30) cc_final: 0.8119 (m-30) REVERT: G 235 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6946 (pp) REVERT: G 330 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9025 (pp) REVERT: G 408 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6542 (pp) REVERT: G 410 LYS cc_start: 0.7418 (pttt) cc_final: 0.6096 (mmtt) REVERT: H 105 ARG cc_start: 0.7419 (mtp-110) cc_final: 0.6732 (ttp80) REVERT: H 170 GLU cc_start: 0.3768 (OUTLIER) cc_final: 0.2658 (tp30) REVERT: H 196 GLU cc_start: 0.7763 (mp0) cc_final: 0.7283 (mt-10) REVERT: H 199 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7501 (mt-10) REVERT: H 217 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.5894 (tp30) REVERT: H 235 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6764 (pp) REVERT: H 286 MET cc_start: 0.8847 (tpp) cc_final: 0.8511 (tpt) REVERT: H 330 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.9017 (pp) REVERT: H 408 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6585 (pp) REVERT: H 410 LYS cc_start: 0.7473 (pttt) cc_final: 0.6013 (mmtt) outliers start: 116 outliers final: 81 residues processed: 602 average time/residue: 0.1837 time to fit residues: 182.9029 Evaluate side-chains 605 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 492 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 142 optimal weight: 0.5980 chunk 251 optimal weight: 0.8980 chunk 279 optimal weight: 0.7980 chunk 280 optimal weight: 5.9990 chunk 348 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 382 optimal weight: 3.9990 chunk 355 optimal weight: 0.6980 chunk 243 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 48 GLN B 112 GLN B 334 GLN C 112 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 334 GLN E 112 GLN F 48 GLN F 112 GLN G 112 GLN G 334 GLN H 48 GLN H 112 GLN H 334 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.156174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.120000 restraints weight = 36447.143| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.36 r_work: 0.3199 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31928 Z= 0.118 Angle : 0.547 6.213 43288 Z= 0.274 Chirality : 0.043 0.134 4928 Planarity : 0.004 0.040 5424 Dihedral : 16.249 174.736 4912 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.55 % Allowed : 15.23 % Favored : 81.22 % 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: -0.52 (0.14), residues: 3960 helix: 1.04 (0.15), residues: 1336 sheet: -1.01 (0.22), residues: 544 loop : -1.07 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 493 TYR 0.027 0.002 TYR G 110 PHE 0.010 0.001 PHE D 401 HIS 0.001 0.000 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00279 (31920) covalent geometry : angle 0.54711 (43288) hydrogen bonds : bond 0.02517 ( 1032) hydrogen bonds : angle 4.31724 ( 2952) Misc. bond : bond 0.00033 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 499 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7497 (mtp-110) cc_final: 0.6784 (ttp80) REVERT: A 170 GLU cc_start: 0.3756 (OUTLIER) cc_final: 0.2680 (tp30) REVERT: A 196 GLU cc_start: 0.7613 (mp0) cc_final: 0.7135 (mt-10) REVERT: A 199 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7251 (mt-10) REVERT: A 232 ASP cc_start: 0.8375 (m-30) cc_final: 0.8156 (m-30) REVERT: A 235 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6951 (pp) REVERT: A 330 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.9016 (pp) REVERT: A 408 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6426 (pp) REVERT: A 410 LYS cc_start: 0.7434 (pttt) cc_final: 0.6030 (mmtt) REVERT: B 105 ARG cc_start: 0.7501 (mtp-110) cc_final: 0.6790 (ttp80) REVERT: B 126 ARG cc_start: 0.5031 (mpt90) cc_final: 0.2351 (mmm-85) REVERT: B 196 GLU cc_start: 0.7677 (mp0) cc_final: 0.7227 (mt-10) REVERT: B 199 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7391 (mt-10) REVERT: B 217 GLU cc_start: 0.6099 (OUTLIER) cc_final: 0.5597 (tp30) REVERT: B 232 ASP cc_start: 0.8353 (m-30) cc_final: 0.8051 (m-30) REVERT: B 235 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6868 (pp) REVERT: B 330 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8959 (pp) REVERT: B 408 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6564 (pp) REVERT: B 410 LYS cc_start: 0.7462 (pttt) cc_final: 0.5936 (mmtt) REVERT: C 105 ARG cc_start: 0.7504 (mtp-110) cc_final: 0.6777 (ttp80) REVERT: C 170 GLU cc_start: 0.3754 (OUTLIER) cc_final: 0.2608 (tp30) REVERT: C 196 GLU cc_start: 0.7553 (mp0) cc_final: 0.7053 (mt-10) REVERT: C 199 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7183 (mt-10) REVERT: C 235 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6948 (pp) REVERT: C 330 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9029 (pp) REVERT: C 399 GLU cc_start: 0.7066 (tp30) cc_final: 0.6629 (mm-30) REVERT: C 408 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6430 (pp) REVERT: C 410 LYS cc_start: 0.7274 (pttt) cc_final: 0.5972 (mmtt) REVERT: D 13 VAL cc_start: 0.8645 (t) cc_final: 0.8346 (p) REVERT: D 196 GLU cc_start: 0.7623 (mp0) cc_final: 0.7128 (mt-10) REVERT: D 199 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7272 (mt-10) REVERT: D 217 GLU cc_start: 0.6271 (OUTLIER) cc_final: 0.5751 (tp30) REVERT: D 232 ASP cc_start: 0.8331 (m-30) cc_final: 0.8124 (m-30) REVERT: D 235 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6796 (pp) REVERT: D 330 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.9050 (pp) REVERT: D 408 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6649 (pp) REVERT: D 410 LYS cc_start: 0.7355 (pttt) cc_final: 0.5894 (mmtt) REVERT: E 105 ARG cc_start: 0.7455 (mtp-110) cc_final: 0.6719 (ttp80) REVERT: E 170 GLU cc_start: 0.3598 (OUTLIER) cc_final: 0.2470 (tp30) REVERT: E 196 GLU cc_start: 0.7667 (mp0) cc_final: 0.7196 (mt-10) REVERT: E 199 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7248 (mt-10) REVERT: E 203 ARG cc_start: 0.7932 (mpt90) cc_final: 0.7092 (mtm110) REVERT: E 235 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6982 (pp) REVERT: E 286 MET cc_start: 0.8836 (tpp) cc_final: 0.8459 (tpt) REVERT: E 330 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8958 (pp) REVERT: E 408 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6389 (pp) REVERT: E 410 LYS cc_start: 0.7340 (pttt) cc_final: 0.6051 (mmtt) REVERT: E 459 TYR cc_start: 0.8763 (t80) cc_final: 0.8491 (t80) REVERT: F 126 ARG cc_start: 0.5059 (mpt90) cc_final: 0.2421 (mmm-85) REVERT: F 196 GLU cc_start: 0.7670 (mp0) cc_final: 0.7208 (mt-10) REVERT: F 199 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7361 (mt-10) REVERT: F 217 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.5769 (tp30) REVERT: F 235 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6809 (pp) REVERT: F 408 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6551 (pp) REVERT: F 410 LYS cc_start: 0.7377 (pttt) cc_final: 0.5978 (mmtt) REVERT: G 150 MET cc_start: 0.7809 (mmm) cc_final: 0.7488 (mmm) REVERT: G 170 GLU cc_start: 0.3407 (OUTLIER) cc_final: 0.2330 (tp30) REVERT: G 196 GLU cc_start: 0.7717 (mp0) cc_final: 0.7213 (mt-10) REVERT: G 199 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7122 (mt-10) REVERT: G 203 ARG cc_start: 0.7832 (mpt180) cc_final: 0.6884 (mtm110) REVERT: G 232 ASP cc_start: 0.8302 (m-30) cc_final: 0.8083 (m-30) REVERT: G 235 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6982 (pp) REVERT: G 330 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8981 (pp) REVERT: G 408 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6430 (pp) REVERT: G 410 LYS cc_start: 0.7311 (pttt) cc_final: 0.6017 (mmtt) REVERT: H 105 ARG cc_start: 0.7375 (mtp-110) cc_final: 0.6679 (ttp80) REVERT: H 170 GLU cc_start: 0.3839 (OUTLIER) cc_final: 0.2823 (tp30) REVERT: H 196 GLU cc_start: 0.7746 (mp0) cc_final: 0.7281 (mt-10) REVERT: H 199 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7424 (mt-10) REVERT: H 217 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5867 (tp30) REVERT: H 235 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6758 (pp) REVERT: H 286 MET cc_start: 0.8770 (tpp) cc_final: 0.8438 (tpt) REVERT: H 330 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.9002 (pp) REVERT: H 408 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6494 (pp) REVERT: H 410 LYS cc_start: 0.7399 (pttt) cc_final: 0.5958 (mmtt) outliers start: 116 outliers final: 84 residues processed: 584 average time/residue: 0.1773 time to fit residues: 170.6307 Evaluate side-chains 598 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 482 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 331 CYS Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 125 optimal weight: 0.9990 chunk 212 optimal weight: 0.1980 chunk 201 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 370 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 175 optimal weight: 0.0050 chunk 46 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 309 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 48 GLN B 112 GLN C 112 GLN C 309 GLN D 112 GLN E 112 GLN F 48 GLN F 112 GLN G 112 GLN H 48 GLN H 112 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.157714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121461 restraints weight = 36300.788| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.37 r_work: 0.3217 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31928 Z= 0.108 Angle : 0.537 6.252 43288 Z= 0.268 Chirality : 0.043 0.132 4928 Planarity : 0.004 0.040 5424 Dihedral : 16.034 174.122 4912 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.31 % Allowed : 15.47 % Favored : 81.22 % 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: -0.42 (0.14), residues: 3960 helix: 1.19 (0.15), residues: 1320 sheet: -0.99 (0.22), residues: 544 loop : -1.05 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 493 TYR 0.023 0.001 TYR G 110 PHE 0.009 0.001 PHE D 401 HIS 0.001 0.000 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00251 (31920) covalent geometry : angle 0.53740 (43288) hydrogen bonds : bond 0.02411 ( 1032) hydrogen bonds : angle 4.26540 ( 2952) Misc. bond : bond 0.00029 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 501 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7454 (mtp-110) cc_final: 0.6751 (ttp80) REVERT: A 150 MET cc_start: 0.7842 (mmm) cc_final: 0.7558 (mmm) REVERT: A 170 GLU cc_start: 0.3752 (OUTLIER) cc_final: 0.2752 (tp30) REVERT: A 196 GLU cc_start: 0.7601 (mp0) cc_final: 0.7128 (mt-10) REVERT: A 199 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7196 (mt-10) REVERT: A 232 ASP cc_start: 0.8382 (m-30) cc_final: 0.8165 (m-30) REVERT: A 235 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6996 (pp) REVERT: A 286 MET cc_start: 0.8783 (tpp) cc_final: 0.8410 (tpt) REVERT: A 330 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9025 (pp) REVERT: A 408 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6439 (pp) REVERT: A 410 LYS cc_start: 0.7366 (pttt) cc_final: 0.6026 (mmtt) REVERT: A 459 TYR cc_start: 0.8735 (t80) cc_final: 0.8405 (t80) REVERT: B 105 ARG cc_start: 0.7478 (mtp-110) cc_final: 0.6778 (ttp80) REVERT: B 126 ARG cc_start: 0.5038 (mpt90) cc_final: 0.2339 (mmm-85) REVERT: B 196 GLU cc_start: 0.7709 (mp0) cc_final: 0.7262 (mt-10) REVERT: B 199 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7326 (mt-10) REVERT: B 217 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.5666 (tp30) REVERT: B 232 ASP cc_start: 0.8363 (m-30) cc_final: 0.8056 (m-30) REVERT: B 235 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6913 (pp) REVERT: B 286 MET cc_start: 0.8851 (tpp) cc_final: 0.8526 (tpt) REVERT: B 330 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8964 (pp) REVERT: B 408 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6551 (pp) REVERT: B 410 LYS cc_start: 0.7431 (pttt) cc_final: 0.5930 (mmtt) REVERT: C 105 ARG cc_start: 0.7513 (mtp-110) cc_final: 0.6779 (ttp80) REVERT: C 170 GLU cc_start: 0.3860 (OUTLIER) cc_final: 0.2698 (tp30) REVERT: C 196 GLU cc_start: 0.7623 (mp0) cc_final: 0.7116 (mt-10) REVERT: C 199 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7208 (mt-10) REVERT: C 235 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7020 (pp) REVERT: C 330 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9021 (pp) REVERT: C 399 GLU cc_start: 0.7021 (tp30) cc_final: 0.6588 (mm-30) REVERT: C 408 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6438 (pp) REVERT: C 410 LYS cc_start: 0.7259 (pttt) cc_final: 0.5967 (mmtt) REVERT: C 459 TYR cc_start: 0.8757 (t80) cc_final: 0.8447 (t80) REVERT: D 13 VAL cc_start: 0.8645 (t) cc_final: 0.8339 (p) REVERT: D 196 GLU cc_start: 0.7669 (mp0) cc_final: 0.7179 (mt-10) REVERT: D 199 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7299 (mt-10) REVERT: D 217 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5741 (tp30) REVERT: D 232 ASP cc_start: 0.8301 (m-30) cc_final: 0.8095 (m-30) REVERT: D 235 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6871 (pp) REVERT: D 330 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9060 (pp) REVERT: D 399 GLU cc_start: 0.7139 (tp30) cc_final: 0.6745 (mm-30) REVERT: D 408 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6650 (pp) REVERT: D 410 LYS cc_start: 0.7326 (pttt) cc_final: 0.5888 (mmtt) REVERT: E 105 ARG cc_start: 0.7421 (mtp-110) cc_final: 0.6697 (ttp80) REVERT: E 149 ARG cc_start: 0.6179 (mpt180) cc_final: 0.5764 (mpt180) REVERT: E 170 GLU cc_start: 0.3617 (OUTLIER) cc_final: 0.2638 (tp30) REVERT: E 196 GLU cc_start: 0.7673 (mp0) cc_final: 0.7199 (mt-10) REVERT: E 199 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7234 (mt-10) REVERT: E 203 ARG cc_start: 0.7887 (mpt90) cc_final: 0.7062 (mtm110) REVERT: E 235 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7024 (pp) REVERT: E 286 MET cc_start: 0.8845 (tpp) cc_final: 0.8460 (tpt) REVERT: E 330 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8932 (pp) REVERT: E 408 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6397 (pp) REVERT: E 410 LYS cc_start: 0.7309 (pttt) cc_final: 0.6002 (mmtt) REVERT: E 459 TYR cc_start: 0.8753 (t80) cc_final: 0.8506 (t80) REVERT: F 149 ARG cc_start: 0.6388 (mpt180) cc_final: 0.6046 (mpt180) REVERT: F 196 GLU cc_start: 0.7691 (mp0) cc_final: 0.7253 (mt-10) REVERT: F 199 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7351 (mt-10) REVERT: F 217 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5753 (tp30) REVERT: F 235 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6883 (pp) REVERT: F 286 MET cc_start: 0.8836 (tpp) cc_final: 0.8555 (tpt) REVERT: F 408 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6580 (pp) REVERT: F 410 LYS cc_start: 0.7371 (pttt) cc_final: 0.5997 (mmtt) REVERT: G 150 MET cc_start: 0.7791 (mmm) cc_final: 0.7512 (mmm) REVERT: G 170 GLU cc_start: 0.3253 (OUTLIER) cc_final: 0.2329 (tp30) REVERT: G 196 GLU cc_start: 0.7699 (mp0) cc_final: 0.7169 (mt-10) REVERT: G 199 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7309 (mt-10) REVERT: G 203 ARG cc_start: 0.7808 (mpt180) cc_final: 0.7543 (mpt180) REVERT: G 232 ASP cc_start: 0.8291 (m-30) cc_final: 0.8077 (m-30) REVERT: G 235 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6994 (pp) REVERT: G 286 MET cc_start: 0.8807 (tpp) cc_final: 0.8449 (tpt) REVERT: G 330 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8971 (pp) REVERT: G 408 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6415 (pp) REVERT: G 410 LYS cc_start: 0.7349 (pttt) cc_final: 0.6052 (mmtt) REVERT: H 105 ARG cc_start: 0.7371 (mtp-110) cc_final: 0.6672 (ttp80) REVERT: H 196 GLU cc_start: 0.7773 (mp0) cc_final: 0.7321 (mt-10) REVERT: H 199 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7422 (mt-10) REVERT: H 217 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.5824 (tp30) REVERT: H 235 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6731 (pp) REVERT: H 286 MET cc_start: 0.8749 (tpp) cc_final: 0.8414 (tpt) REVERT: H 330 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8990 (pp) REVERT: H 408 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6494 (pp) REVERT: H 410 LYS cc_start: 0.7389 (pttt) cc_final: 0.5955 (mmtt) REVERT: H 412 ARG cc_start: 0.8332 (ptp90) cc_final: 0.7959 (ptp90) outliers start: 108 outliers final: 75 residues processed: 583 average time/residue: 0.1904 time to fit residues: 182.8939 Evaluate side-chains 590 residues out of total 3264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 484 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 331 CYS Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 267 optimal weight: 0.7980 chunk 292 optimal weight: 0.2980 chunk 96 optimal weight: 6.9990 chunk 389 optimal weight: 1.9990 chunk 368 optimal weight: 1.9990 chunk 296 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 17 optimal weight: 0.0270 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 112 GLN B 334 GLN C 112 GLN C 309 GLN D 112 GLN E 112 GLN F 48 GLN F 112 GLN F 334 GLN G 112 GLN G 334 GLN H 112 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.156124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119828 restraints weight = 36593.090| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.36 r_work: 0.3200 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31928 Z= 0.122 Angle : 0.549 6.233 43288 Z= 0.274 Chirality : 0.043 0.134 4928 Planarity : 0.004 0.040 5424 Dihedral : 15.895 173.773 4908 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.52 % Allowed : 15.13 % Favored : 81.34 % 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: -0.42 (0.14), residues: 3960 helix: 1.15 (0.15), residues: 1328 sheet: -0.99 (0.22), residues: 544 loop : -1.02 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 493 TYR 0.026 0.002 TYR C 110 PHE 0.009 0.001 PHE D 401 HIS 0.001 0.000 HIS G 466 Details of bonding type rmsd covalent geometry : bond 0.00291 (31920) covalent geometry : angle 0.54854 (43288) hydrogen bonds : bond 0.02553 ( 1032) hydrogen bonds : angle 4.27749 ( 2952) Misc. bond : bond 0.00039 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8506.11 seconds wall clock time: 146 minutes 24.92 seconds (8784.92 seconds total)