Starting phenix.real_space_refine on Mon Sep 14 18:29:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u9o_20701/09_2026/6u9o_20701.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u9o_20701/09_2026/6u9o_20701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u9o_20701/09_2026/6u9o_20701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u9o_20701/09_2026/6u9o_20701.map" model { file = "/net/cci-nas-00/data/ceres_data/6u9o_20701/09_2026/6u9o_20701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u9o_20701/09_2026/6u9o_20701.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6u9o_20701/09_2026/6u9o_20701.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u9o_20701/09_2026/6u9o_20701.cif" } resolution = 3.36 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= 0.068 sd= 2.635 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 96 5.49 5 S 176 5.16 5 C 19736 2.51 5 N 5440 2.21 5 O 6344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31792 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "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: "B" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "C" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "K" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "D" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "E" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "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: "F" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "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: "G" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "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: "H" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "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: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Time building chain proxies: 6.01, per 1000 atoms: 0.19 Number of scatterers: 31792 At special positions: 0 Unit cell: (152.25, 152.25, 116.55, 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 96 15.00 O 6344 8.00 N 5440 7.00 C 19736 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: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7280 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 48 sheets defined 37.5% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.917A pdb=" N PHE A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.612A pdb=" N ASP A 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE A 163 " --> pdb=" O SER A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 163' Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.732A pdb=" N ASP A 184 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.542A pdb=" N ALA A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.793A pdb=" N LYS A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.741A pdb=" N LEU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.819A pdb=" N ILE A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.640A pdb=" N ALA A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 355 removed outlier: 3.538A pdb=" N SER A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.820A pdb=" N ILE A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 455 Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 475 through 486 Processing helix chain 'A' and resid 496 through 502 removed outlier: 3.698A 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 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 127 through 138 removed outlier: 3.918A pdb=" N PHE B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 removed outlier: 3.611A pdb=" N ASP B 162 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE B 163 " --> pdb=" O SER B 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 159 through 163' Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.733A pdb=" N ASP B 184 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 203 removed outlier: 3.543A pdb=" N ALA B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.792A pdb=" N LYS B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 256 through 267 removed outlier: 3.740A pdb=" N LEU B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.819A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.639A pdb=" N ALA B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.538A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.821A pdb=" N ILE B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 455 Processing helix chain 'B' and resid 456 through 472 Processing helix chain 'B' and resid 475 through 486 Processing helix chain 'B' and resid 496 through 502 removed outlier: 3.699A 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 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 127 through 138 removed outlier: 3.917A pdb=" N PHE C 131 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.612A pdb=" N ASP C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE C 163 " --> pdb=" O SER C 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 181 through 185 removed outlier: 3.732A pdb=" N ASP C 184 " --> pdb=" O LYS C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 203 removed outlier: 3.542A pdb=" N ALA C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 removed outlier: 3.793A pdb=" N LYS C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 267 removed outlier: 3.741A pdb=" N LEU C 262 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.819A pdb=" N ILE C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.639A pdb=" N ALA C 310 " --> pdb=" O THR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 342 through 355 removed outlier: 3.538A pdb=" N SER C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.820A pdb=" N ILE C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 455 Processing helix chain 'C' and resid 456 through 472 Processing helix chain 'C' and resid 475 through 486 Processing helix chain 'C' and resid 496 through 502 removed outlier: 3.698A 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 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 127 through 138 removed outlier: 3.917A pdb=" N PHE D 131 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.612A pdb=" N ASP D 162 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE D 163 " --> pdb=" O SER D 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 159 through 163' Processing helix chain 'D' and resid 181 through 185 removed outlier: 3.733A pdb=" N ASP D 184 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 203 removed outlier: 3.542A pdb=" N ALA D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.793A pdb=" N LYS D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 267 removed outlier: 3.741A pdb=" N LEU D 262 " --> pdb=" O TYR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.819A pdb=" N ILE D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.639A pdb=" N ALA D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 355 removed outlier: 3.538A pdb=" N SER D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.820A pdb=" N ILE D 373 " --> pdb=" O ASN D 369 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 379 " --> pdb=" O LYS D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 456 through 472 Processing helix chain 'D' and resid 475 through 486 Processing helix chain 'D' and resid 496 through 502 removed outlier: 3.698A 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 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 127 through 138 removed outlier: 3.918A pdb=" N PHE E 131 " --> pdb=" O VAL E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 removed outlier: 3.611A pdb=" N ASP E 162 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE E 163 " --> pdb=" O SER E 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 159 through 163' Processing helix chain 'E' and resid 181 through 185 removed outlier: 3.732A pdb=" N ASP E 184 " --> pdb=" O LYS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 203 removed outlier: 3.543A pdb=" N ALA E 197 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 233 removed outlier: 3.793A pdb=" N LYS E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 256 through 267 removed outlier: 3.741A pdb=" N LEU E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.820A pdb=" N ILE E 284 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 removed outlier: 3.639A pdb=" N ALA E 310 " --> pdb=" O THR E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 355 removed outlier: 3.538A pdb=" N SER E 351 " --> pdb=" O VAL E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.820A pdb=" N ILE E 373 " --> pdb=" O ASN E 369 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 379 " --> pdb=" O LYS E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'E' and resid 456 through 472 Processing helix chain 'E' and resid 475 through 486 Processing helix chain 'E' and resid 496 through 502 removed outlier: 3.698A 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 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 75 through 85 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 127 through 138 removed outlier: 3.917A pdb=" N PHE F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.613A pdb=" N ASP F 162 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE F 163 " --> pdb=" O SER F 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 163' Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.732A pdb=" N ASP F 184 " --> pdb=" O LYS F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 203 removed outlier: 3.543A pdb=" N ALA F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 233 removed outlier: 3.793A pdb=" N LYS F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 256 through 267 removed outlier: 3.740A pdb=" N LEU F 262 " --> pdb=" O TYR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 removed outlier: 3.819A pdb=" N ILE F 284 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 removed outlier: 3.639A pdb=" N ALA F 310 " --> pdb=" O THR F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 355 removed outlier: 3.538A pdb=" N SER F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.821A pdb=" N ILE F 373 " --> pdb=" O ASN F 369 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU F 379 " --> pdb=" O LYS F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 456 through 472 Processing helix chain 'F' and resid 475 through 486 Processing helix chain 'F' and resid 496 through 502 removed outlier: 3.698A 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 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 127 through 138 removed outlier: 3.917A pdb=" N PHE G 131 " --> pdb=" O VAL G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 removed outlier: 3.612A pdb=" N ASP G 162 " --> pdb=" O SER G 159 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE G 163 " --> pdb=" O SER G 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 159 through 163' Processing helix chain 'G' and resid 181 through 185 removed outlier: 3.733A pdb=" N ASP G 184 " --> pdb=" O LYS G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 203 removed outlier: 3.542A pdb=" N ALA G 197 " --> pdb=" O THR G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 233 removed outlier: 3.794A pdb=" N LYS G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 255 No H-bonds generated for 'chain 'G' and resid 253 through 255' Processing helix chain 'G' and resid 256 through 267 removed outlier: 3.741A pdb=" N LEU G 262 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 removed outlier: 3.820A pdb=" N ILE G 284 " --> pdb=" O SER G 280 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 315 removed outlier: 3.639A pdb=" N ALA G 310 " --> pdb=" O THR G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 342 through 355 removed outlier: 3.539A pdb=" N SER G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 removed outlier: 3.821A pdb=" N ILE G 373 " --> pdb=" O ASN G 369 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU G 379 " --> pdb=" O LYS G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 455 Processing helix chain 'G' and resid 456 through 472 Processing helix chain 'G' and resid 475 through 486 Processing helix chain 'G' and resid 496 through 502 removed outlier: 3.699A 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 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 75 through 85 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 127 through 138 removed outlier: 3.918A pdb=" N PHE H 131 " --> pdb=" O VAL H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 163 removed outlier: 3.612A pdb=" N ASP H 162 " --> pdb=" O SER H 159 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE H 163 " --> pdb=" O SER H 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 159 through 163' Processing helix chain 'H' and resid 181 through 185 removed outlier: 3.733A pdb=" N ASP H 184 " --> pdb=" O LYS H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 203 removed outlier: 3.543A pdb=" N ALA H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 233 removed outlier: 3.793A pdb=" N LYS H 228 " --> pdb=" O ARG H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 255 No H-bonds generated for 'chain 'H' and resid 253 through 255' Processing helix chain 'H' and resid 256 through 267 removed outlier: 3.741A pdb=" N LEU H 262 " --> pdb=" O TYR H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 removed outlier: 3.819A pdb=" N ILE H 284 " --> pdb=" O SER H 280 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 315 removed outlier: 3.640A pdb=" N ALA H 310 " --> pdb=" O THR H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 342 through 355 removed outlier: 3.538A pdb=" N SER H 351 " --> pdb=" O VAL H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 removed outlier: 3.821A pdb=" N ILE H 373 " --> pdb=" O ASN H 369 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU H 379 " --> pdb=" O LYS H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 455 Processing helix chain 'H' and resid 456 through 472 Processing helix chain 'H' and resid 475 through 486 Processing helix chain 'H' and resid 496 through 502 removed outlier: 3.698A pdb=" N GLY H 502 " --> pdb=" O GLN H 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 4.607A pdb=" N LYS D 489 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 38 removed outlier: 4.606A pdb=" N LYS A 489 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N GLY B 29 " --> pdb=" O PHE A 490 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LYS A 492 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.481A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.924A pdb=" N ILE A 142 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ILE A 157 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE A 144 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 188 through 189 removed outlier: 5.748A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 401 through 403 Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 38 removed outlier: 4.607A pdb=" N LYS B 489 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLY C 29 " --> pdb=" O PHE B 490 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LYS B 492 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.481A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ARG B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.923A pdb=" N ILE B 142 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE B 157 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE B 144 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 188 through 189 removed outlier: 5.747A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 401 through 403 Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 38 removed outlier: 4.606A pdb=" N LYS C 489 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLY D 29 " --> pdb=" O PHE C 490 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LYS C 492 " --> pdb=" O GLY D 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.481A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 142 through 145 removed outlier: 6.923A pdb=" N ILE C 142 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ILE C 157 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 144 " --> pdb=" O VAL C 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 188 through 189 removed outlier: 5.748A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 401 through 403 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.481A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 142 through 145 removed outlier: 6.923A pdb=" N ILE D 142 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ILE D 157 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE D 144 " --> pdb=" O VAL D 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 188 through 189 removed outlier: 5.748A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 401 through 403 Processing sheet with id=AC7, first strand: chain 'E' and resid 28 through 29 removed outlier: 4.605A pdb=" N LYS H 489 " --> pdb=" O LEU H 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 35 through 38 removed outlier: 4.605A pdb=" N LYS E 489 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY F 29 " --> pdb=" O PHE E 490 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LYS E 492 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.481A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 142 through 145 removed outlier: 6.924A pdb=" N ILE E 142 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ILE E 157 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE E 144 " --> pdb=" O VAL E 155 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 188 through 189 removed outlier: 5.748A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 401 through 403 Processing sheet with id=AD5, first strand: chain 'F' and resid 35 through 38 removed outlier: 4.606A pdb=" N LYS F 489 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N GLY G 29 " --> pdb=" O PHE F 490 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LYS F 492 " --> pdb=" O GLY G 29 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.481A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ARG F 322 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY F 301 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE F 91 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 142 through 145 removed outlier: 6.924A pdb=" N ILE F 142 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ILE F 157 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE F 144 " --> pdb=" O VAL F 155 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 188 through 189 removed outlier: 5.748A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 401 through 403 Processing sheet with id=AE2, first strand: chain 'G' and resid 35 through 38 removed outlier: 4.606A pdb=" N LYS G 489 " --> pdb=" O LEU G 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE4, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.481A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 142 through 145 removed outlier: 6.923A pdb=" N ILE G 142 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE G 157 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE G 144 " --> pdb=" O VAL G 155 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 188 through 189 removed outlier: 5.748A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 401 through 403 Processing sheet with id=AE8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.481A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 142 through 145 removed outlier: 6.924A pdb=" N ILE H 142 " --> pdb=" O ILE H 157 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE H 157 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE H 144 " --> pdb=" O VAL H 155 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 188 through 189 removed outlier: 5.747A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 401 through 403 992 hydrogen bonds defined for protein. 2832 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.58 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5337 1.30 - 1.43: 7871 1.43 - 1.56: 18600 1.56 - 1.69: 248 1.69 - 1.82: 296 Bond restraints: 32352 Sorted by residual: bond pdb=" C2' ATP H 603 " pdb=" C3' ATP H 603 " ideal model delta sigma weight residual 1.531 1.246 0.285 1.20e-02 6.94e+03 5.63e+02 bond pdb=" C2' ATP E 603 " pdb=" C3' ATP E 603 " ideal model delta sigma weight residual 1.531 1.247 0.284 1.20e-02 6.94e+03 5.61e+02 bond pdb=" C2' ATP A 603 " pdb=" C3' ATP A 603 " ideal model delta sigma weight residual 1.531 1.247 0.284 1.20e-02 6.94e+03 5.60e+02 bond pdb=" C2' ATP B 603 " pdb=" C3' ATP B 603 " ideal model delta sigma weight residual 1.531 1.247 0.284 1.20e-02 6.94e+03 5.60e+02 bond pdb=" C2' ATP F 603 " pdb=" C3' ATP F 603 " ideal model delta sigma weight residual 1.531 1.247 0.284 1.20e-02 6.94e+03 5.58e+02 ... (remaining 32347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 42798 4.11 - 8.22: 810 8.22 - 12.33: 212 12.33 - 16.44: 68 16.44 - 20.55: 48 Bond angle restraints: 43936 Sorted by residual: angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 121.24 18.63 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PB ATP C 603 " pdb=" O3B ATP C 603 " pdb=" PG ATP C 603 " ideal model delta sigma weight residual 139.87 121.25 18.62 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 121.26 18.61 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 121.27 18.60 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PB ATP H 603 " pdb=" O3B ATP H 603 " pdb=" PG ATP H 603 " ideal model delta sigma weight residual 139.87 121.28 18.59 1.00e+00 1.00e+00 3.46e+02 ... (remaining 43931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 18504 33.93 - 67.87: 568 67.87 - 101.80: 48 101.80 - 135.74: 16 135.74 - 169.67: 24 Dihedral angle restraints: 19160 sinusoidal: 7752 harmonic: 11408 Sorted by residual: dihedral pdb=" CA THR G 74 " pdb=" C THR G 74 " pdb=" N GLU G 75 " pdb=" CA GLU G 75 " ideal model delta harmonic sigma weight residual 180.00 142.19 37.81 0 5.00e+00 4.00e-02 5.72e+01 dihedral pdb=" CA THR A 74 " pdb=" C THR A 74 " pdb=" N GLU A 75 " pdb=" CA GLU A 75 " ideal model delta harmonic sigma weight residual 180.00 142.24 37.76 0 5.00e+00 4.00e-02 5.70e+01 dihedral pdb=" CA THR E 74 " pdb=" C THR E 74 " pdb=" N GLU E 75 " pdb=" CA GLU E 75 " ideal model delta harmonic sigma weight residual 180.00 142.24 37.76 0 5.00e+00 4.00e-02 5.70e+01 ... (remaining 19157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3525 0.070 - 0.140: 1239 0.140 - 0.209: 188 0.209 - 0.279: 24 0.279 - 0.349: 24 Chirality restraints: 5000 Sorted by residual: chirality pdb=" C3D NAD D 605 " pdb=" C2D NAD D 605 " pdb=" C4D NAD D 605 " pdb=" O3D NAD D 605 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" C3D NAD G 605 " pdb=" C2D NAD G 605 " pdb=" C4D NAD G 605 " pdb=" O3D NAD G 605 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C3D NAD B 605 " pdb=" C2D NAD B 605 " pdb=" C4D NAD B 605 " pdb=" O3D NAD B 605 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 4997 not shown) Planarity restraints: 5456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 109 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.39e+00 pdb=" C LYS B 109 " -0.053 2.00e-02 2.50e+03 pdb=" O LYS B 109 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR B 110 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 109 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.38e+00 pdb=" C LYS A 109 " -0.053 2.00e-02 2.50e+03 pdb=" O LYS A 109 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 110 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 109 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.28e+00 pdb=" C LYS G 109 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS G 109 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR G 110 " -0.018 2.00e-02 2.50e+03 ... (remaining 5453 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2663 2.72 - 3.27: 30606 3.27 - 3.81: 55327 3.81 - 4.36: 66874 4.36 - 4.90: 109466 Nonbonded interactions: 264936 Sorted by model distance: nonbonded pdb=" OE1 GLU B 500 " pdb=" OG1 THR C 31 " model vdw 2.177 3.040 nonbonded pdb=" OG1 THR A 31 " pdb=" OE1 GLU D 500 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR E 31 " pdb=" OE1 GLU H 500 " model vdw 2.207 3.040 nonbonded pdb=" OE1 GLU F 500 " pdb=" OG1 THR G 31 " model vdw 2.215 3.040 nonbonded pdb=" OE1 GLU E 500 " pdb=" OG1 THR F 31 " model vdw 2.224 3.040 ... (remaining 264931 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: 0.11 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: 2.690 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.860 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 : 0.018 0.287 32360 Z= 0.971 Angle : 1.675 20.547 43936 Z= 0.941 Chirality : 0.071 0.349 5000 Planarity : 0.007 0.043 5456 Dihedral : 17.194 169.672 11880 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 8.31 % Allowed : 8.80 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.12 (0.11), residues: 3968 helix: -3.34 (0.09), residues: 1296 sheet: -2.04 (0.24), residues: 384 loop : -2.53 (0.11), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG G 231 TYR 0.019 0.003 TYR F 411 PHE 0.027 0.004 PHE E 401 HIS 0.006 0.002 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.01762 / 0.97 (32352) covalent geometry : angle 1.67536 / 0.94 (43936) hydrogen bonds : bond 0.19530 / 13.28 ( 992) hydrogen bonds : angle 8.35689 / 5.79 ( 2832) Misc. bond : bond 0.00091 / 0.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1735 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 272 poor density : 1463 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8338 (t0) cc_final: 0.7959 (t0) REVERT: A 75 GLU cc_start: 0.8093 (mp0) cc_final: 0.7675 (mp0) REVERT: A 108 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.8926 (tppp) REVERT: A 111 GLU cc_start: 0.9298 (mm-30) cc_final: 0.9020 (mm-30) REVERT: A 164 ASP cc_start: 0.7999 (t70) cc_final: 0.7171 (t70) REVERT: A 168 GLU cc_start: 0.8851 (mp0) cc_final: 0.8404 (pm20) REVERT: A 175 LEU cc_start: 0.9578 (mp) cc_final: 0.9357 (mp) REVERT: A 179 MET cc_start: 0.8551 (ptt) cc_final: 0.8258 (ptt) REVERT: A 209 LEU cc_start: 0.7900 (pp) cc_final: 0.7687 (pp) REVERT: A 216 ASP cc_start: 0.9084 (t70) cc_final: 0.8697 (t0) REVERT: A 222 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8047 (mm) REVERT: A 253 HIS cc_start: 0.7574 (m-70) cc_final: 0.6950 (m-70) REVERT: A 258 TYR cc_start: 0.8837 (t80) cc_final: 0.8597 (t80) REVERT: A 261 ASP cc_start: 0.8831 (p0) cc_final: 0.8234 (p0) REVERT: A 262 LEU cc_start: 0.9065 (mm) cc_final: 0.8823 (mp) REVERT: A 269 ASP cc_start: 0.8347 (m-30) cc_final: 0.8080 (m-30) REVERT: A 274 ASP cc_start: 0.8831 (t0) cc_final: 0.8588 (t0) REVERT: A 296 ASN cc_start: 0.9206 (p0) cc_final: 0.8998 (p0) REVERT: A 329 SER cc_start: 0.9377 (p) cc_final: 0.9116 (p) REVERT: A 330 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9116 (pp) REVERT: A 335 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7211 (mm-30) REVERT: A 410 LYS cc_start: 0.7853 (pttt) cc_final: 0.7056 (mtpp) REVERT: A 411 TYR cc_start: 0.8797 (t80) cc_final: 0.8425 (t80) REVERT: B 15 ASP cc_start: 0.8293 (t0) cc_final: 0.8018 (t0) REVERT: B 75 GLU cc_start: 0.7960 (mp0) cc_final: 0.7569 (mp0) REVERT: B 108 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.8940 (tppp) REVERT: B 128 ARG cc_start: 0.7887 (ptt-90) cc_final: 0.7240 (ptt-90) REVERT: B 164 ASP cc_start: 0.8122 (t70) cc_final: 0.6403 (t70) REVERT: B 168 GLU cc_start: 0.8773 (mp0) cc_final: 0.8309 (pm20) REVERT: B 175 LEU cc_start: 0.9455 (mp) cc_final: 0.9205 (mp) REVERT: B 179 MET cc_start: 0.8421 (ptt) cc_final: 0.8187 (ptt) REVERT: B 216 ASP cc_start: 0.9023 (t70) cc_final: 0.8593 (t0) REVERT: B 222 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8061 (mm) REVERT: B 253 HIS cc_start: 0.7484 (m-70) cc_final: 0.6938 (m-70) REVERT: B 258 TYR cc_start: 0.8667 (t80) cc_final: 0.8346 (t80) REVERT: B 269 ASP cc_start: 0.8274 (m-30) cc_final: 0.7985 (m-30) REVERT: B 312 ASN cc_start: 0.9203 (t0) cc_final: 0.8847 (t0) REVERT: B 329 SER cc_start: 0.9366 (p) cc_final: 0.9141 (p) REVERT: B 330 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9125 (pp) REVERT: B 410 LYS cc_start: 0.7791 (pttt) cc_final: 0.6930 (mtpp) REVERT: B 411 TYR cc_start: 0.8703 (t80) cc_final: 0.8423 (t80) REVERT: C 15 ASP cc_start: 0.8339 (t0) cc_final: 0.8000 (t0) REVERT: C 75 GLU cc_start: 0.8067 (mp0) cc_final: 0.7678 (mp0) REVERT: C 108 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.8962 (tppp) REVERT: C 111 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8046 (mm-30) REVERT: C 164 ASP cc_start: 0.7984 (t70) cc_final: 0.7425 (t0) REVERT: C 168 GLU cc_start: 0.8763 (mp0) cc_final: 0.8266 (pm20) REVERT: C 179 MET cc_start: 0.8416 (ptt) cc_final: 0.8125 (ptt) REVERT: C 209 LEU cc_start: 0.7947 (pp) cc_final: 0.7731 (pp) REVERT: C 216 ASP cc_start: 0.9088 (t70) cc_final: 0.8609 (t0) REVERT: C 222 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8008 (mm) REVERT: C 253 HIS cc_start: 0.7679 (m-70) cc_final: 0.7080 (m-70) REVERT: C 258 TYR cc_start: 0.8823 (t80) cc_final: 0.8410 (t80) REVERT: C 261 ASP cc_start: 0.8752 (p0) cc_final: 0.8109 (p0) REVERT: C 262 LEU cc_start: 0.8995 (mm) cc_final: 0.8563 (tp) REVERT: C 269 ASP cc_start: 0.8289 (m-30) cc_final: 0.8039 (m-30) REVERT: C 274 ASP cc_start: 0.8845 (t0) cc_final: 0.8604 (t0) REVERT: C 330 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9153 (pp) REVERT: C 335 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6904 (mm-30) REVERT: C 410 LYS cc_start: 0.7858 (pttt) cc_final: 0.7071 (mtpp) REVERT: C 411 TYR cc_start: 0.8781 (t80) cc_final: 0.8428 (t80) REVERT: D 15 ASP cc_start: 0.8337 (t0) cc_final: 0.8063 (t0) REVERT: D 51 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8967 (pp) REVERT: D 75 GLU cc_start: 0.7976 (mp0) cc_final: 0.7572 (mp0) REVERT: D 102 ASN cc_start: 0.9154 (t0) cc_final: 0.8818 (t0) REVERT: D 108 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.8945 (tppp) REVERT: D 128 ARG cc_start: 0.7885 (ptt-90) cc_final: 0.7268 (ptt-90) REVERT: D 164 ASP cc_start: 0.8095 (t70) cc_final: 0.7586 (t0) REVERT: D 168 GLU cc_start: 0.8799 (mp0) cc_final: 0.8354 (pm20) REVERT: D 175 LEU cc_start: 0.9519 (mp) cc_final: 0.9240 (mp) REVERT: D 179 MET cc_start: 0.8507 (ptt) cc_final: 0.8243 (ptt) REVERT: D 205 LYS cc_start: 0.9159 (mptm) cc_final: 0.8813 (mptt) REVERT: D 209 LEU cc_start: 0.7975 (pp) cc_final: 0.7768 (pp) REVERT: D 216 ASP cc_start: 0.9024 (t70) cc_final: 0.8637 (t0) REVERT: D 222 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8133 (mm) REVERT: D 253 HIS cc_start: 0.7607 (m-70) cc_final: 0.7042 (m-70) REVERT: D 269 ASP cc_start: 0.8286 (m-30) cc_final: 0.8059 (m-30) REVERT: D 274 ASP cc_start: 0.8797 (t0) cc_final: 0.8595 (t0) REVERT: D 312 ASN cc_start: 0.9194 (t0) cc_final: 0.8856 (t0) REVERT: D 329 SER cc_start: 0.9385 (p) cc_final: 0.9155 (p) REVERT: D 330 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9134 (pp) REVERT: D 335 GLU cc_start: 0.7527 (mm-30) cc_final: 0.6900 (mm-30) REVERT: D 395 GLU cc_start: 0.8534 (mp0) cc_final: 0.8330 (mp0) REVERT: D 410 LYS cc_start: 0.7714 (pttt) cc_final: 0.6808 (mtpp) REVERT: D 411 TYR cc_start: 0.8711 (t80) cc_final: 0.8369 (t80) REVERT: E 15 ASP cc_start: 0.8302 (t0) cc_final: 0.8029 (t0) REVERT: E 34 ASP cc_start: 0.8665 (p0) cc_final: 0.8420 (p0) REVERT: E 75 GLU cc_start: 0.8004 (mp0) cc_final: 0.7634 (mp0) REVERT: E 108 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.8941 (tppp) REVERT: E 111 GLU cc_start: 0.9279 (mm-30) cc_final: 0.9012 (mm-30) REVERT: E 168 GLU cc_start: 0.8803 (mp0) cc_final: 0.8365 (pm20) REVERT: E 179 MET cc_start: 0.8367 (ptt) cc_final: 0.8091 (ptt) REVERT: E 209 LEU cc_start: 0.7917 (pp) cc_final: 0.7680 (pp) REVERT: E 216 ASP cc_start: 0.9079 (t70) cc_final: 0.8611 (t0) REVERT: E 222 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8030 (mm) REVERT: E 253 HIS cc_start: 0.7523 (m-70) cc_final: 0.6947 (m-70) REVERT: E 258 TYR cc_start: 0.8790 (t80) cc_final: 0.8473 (t80) REVERT: E 261 ASP cc_start: 0.8735 (p0) cc_final: 0.8034 (p0) REVERT: E 262 LEU cc_start: 0.9012 (mm) cc_final: 0.8605 (tp) REVERT: E 269 ASP cc_start: 0.8321 (m-30) cc_final: 0.8038 (m-30) REVERT: E 274 ASP cc_start: 0.8851 (t0) cc_final: 0.8635 (t0) REVERT: E 325 MET cc_start: 0.8740 (ttm) cc_final: 0.8428 (ttp) REVERT: E 329 SER cc_start: 0.9383 (p) cc_final: 0.9166 (p) REVERT: E 330 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9139 (pp) REVERT: E 335 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7184 (mm-30) REVERT: E 395 GLU cc_start: 0.8481 (mp0) cc_final: 0.8280 (mp0) REVERT: E 411 TYR cc_start: 0.8775 (t80) cc_final: 0.8452 (t80) REVERT: F 15 ASP cc_start: 0.8315 (t0) cc_final: 0.8056 (t0) REVERT: F 51 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8967 (pp) REVERT: F 75 GLU cc_start: 0.7914 (mp0) cc_final: 0.7535 (mp0) REVERT: F 105 ARG cc_start: 0.8133 (mtm110) cc_final: 0.7924 (ttp-110) REVERT: F 108 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8877 (tppp) REVERT: F 128 ARG cc_start: 0.7923 (ptt-90) cc_final: 0.7236 (ptt-90) REVERT: F 168 GLU cc_start: 0.8793 (mp0) cc_final: 0.8307 (pm20) REVERT: F 175 LEU cc_start: 0.9452 (mp) cc_final: 0.9200 (mp) REVERT: F 179 MET cc_start: 0.8445 (ptt) cc_final: 0.8201 (ptt) REVERT: F 216 ASP cc_start: 0.9045 (t70) cc_final: 0.8556 (t0) REVERT: F 222 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8050 (mm) REVERT: F 253 HIS cc_start: 0.7598 (m-70) cc_final: 0.6972 (m-70) REVERT: F 269 ASP cc_start: 0.8270 (m-30) cc_final: 0.8023 (m-30) REVERT: F 274 ASP cc_start: 0.8805 (t0) cc_final: 0.8599 (t0) REVERT: F 329 SER cc_start: 0.9389 (p) cc_final: 0.9139 (p) REVERT: F 330 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9145 (pp) REVERT: F 335 GLU cc_start: 0.7457 (mm-30) cc_final: 0.6833 (mm-30) REVERT: F 395 GLU cc_start: 0.8472 (mp0) cc_final: 0.8248 (mp0) REVERT: F 411 TYR cc_start: 0.8719 (t80) cc_final: 0.8379 (t80) REVERT: F 505 SER cc_start: 0.9032 (t) cc_final: 0.8816 (p) REVERT: G 15 ASP cc_start: 0.8336 (t0) cc_final: 0.8087 (t0) REVERT: G 34 ASP cc_start: 0.8706 (p0) cc_final: 0.8482 (p0) REVERT: G 75 GLU cc_start: 0.8085 (mp0) cc_final: 0.7697 (mp0) REVERT: G 108 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.8931 (tppp) REVERT: G 111 GLU cc_start: 0.9290 (mm-30) cc_final: 0.9042 (mm-30) REVERT: G 168 GLU cc_start: 0.8751 (mp0) cc_final: 0.8348 (pm20) REVERT: G 175 LEU cc_start: 0.9560 (mp) cc_final: 0.9336 (mp) REVERT: G 179 MET cc_start: 0.8533 (ptt) cc_final: 0.8266 (ptt) REVERT: G 209 LEU cc_start: 0.7868 (pp) cc_final: 0.7633 (pp) REVERT: G 216 ASP cc_start: 0.9072 (t70) cc_final: 0.8628 (t0) REVERT: G 222 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8029 (mm) REVERT: G 253 HIS cc_start: 0.7654 (m-70) cc_final: 0.7051 (m-70) REVERT: G 269 ASP cc_start: 0.8347 (m-30) cc_final: 0.8114 (m-30) REVERT: G 274 ASP cc_start: 0.8838 (t0) cc_final: 0.8593 (t0) REVERT: G 330 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9162 (pp) REVERT: G 335 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7132 (mm-30) REVERT: G 395 GLU cc_start: 0.8509 (mp0) cc_final: 0.8303 (mp0) REVERT: G 410 LYS cc_start: 0.7794 (pttt) cc_final: 0.6996 (mtpp) REVERT: G 411 TYR cc_start: 0.8746 (t80) cc_final: 0.8414 (t80) REVERT: O 1 MET cc_start: 0.5763 (pp-130) cc_final: 0.5550 (pmm) REVERT: H 15 ASP cc_start: 0.8320 (t0) cc_final: 0.8087 (t0) REVERT: H 51 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8859 (pp) REVERT: H 75 GLU cc_start: 0.7933 (mp0) cc_final: 0.7530 (mp0) REVERT: H 108 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.8911 (tppp) REVERT: H 128 ARG cc_start: 0.7855 (ptt-90) cc_final: 0.7247 (ptt-90) REVERT: H 150 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8123 (tmm) REVERT: H 164 ASP cc_start: 0.8127 (t70) cc_final: 0.7642 (t0) REVERT: H 166 LEU cc_start: 0.8825 (mp) cc_final: 0.8457 (mt) REVERT: H 168 GLU cc_start: 0.8755 (mp0) cc_final: 0.8391 (pm20) REVERT: H 175 LEU cc_start: 0.9503 (mp) cc_final: 0.9262 (mp) REVERT: H 179 MET cc_start: 0.8495 (ptt) cc_final: 0.8264 (ptt) REVERT: H 216 ASP cc_start: 0.9079 (t70) cc_final: 0.8644 (t0) REVERT: H 222 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8089 (mm) REVERT: H 253 HIS cc_start: 0.7582 (m-70) cc_final: 0.6991 (m-70) REVERT: H 261 ASP cc_start: 0.8609 (p0) cc_final: 0.8367 (p0) REVERT: H 269 ASP cc_start: 0.8328 (m-30) cc_final: 0.8113 (m-30) REVERT: H 274 ASP cc_start: 0.8790 (t0) cc_final: 0.8589 (t0) REVERT: H 329 SER cc_start: 0.9362 (p) cc_final: 0.9084 (p) REVERT: H 330 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9127 (pp) REVERT: H 395 GLU cc_start: 0.8510 (mp0) cc_final: 0.8281 (mp0) REVERT: H 411 TYR cc_start: 0.8724 (t80) cc_final: 0.8418 (t80) REVERT: H 505 SER cc_start: 0.9032 (t) cc_final: 0.8718 (t) outliers start: 272 outliers final: 78 residues processed: 1516 average time/residue: 0.1795 time to fit residues: 447.8324 Evaluate side-chains 1045 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 939 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain E residue 108 LYS Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain F residue 467 SER Chi-restraints excluded: chain F residue 508 SER Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain G residue 467 SER Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 508 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.0670 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN A 102 ASN A 230 ASN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 102 ASN B 230 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN C 230 ASN ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN D 230 ASN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN D 303 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN E 230 ASN ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN F 230 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 230 ASN ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN H 230 ASN ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.142190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110012 restraints weight = 50559.021| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.30 r_work: 0.3135 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32360 Z= 0.138 Angle : 0.737 7.236 43936 Z= 0.361 Chirality : 0.049 0.192 5000 Planarity : 0.005 0.061 5456 Dihedral : 16.948 160.429 4895 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 6.42 % Allowed : 18.98 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.90 (0.12), residues: 3968 helix: -1.71 (0.12), residues: 1320 sheet: -2.08 (0.22), residues: 480 loop : -2.02 (0.12), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 136 TYR 0.013 0.001 TYR A 353 PHE 0.020 0.001 PHE C 401 HIS 0.003 0.001 HIS D 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (32352) covalent geometry : angle 0.73693 / 0.36 (43936) hydrogen bonds : bond 0.04207 / 2.80 ( 992) hydrogen bonds : angle 5.77233 / 3.98 ( 2832) Misc. bond : bond 0.00049 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1366 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 1156 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8912 (p0) cc_final: 0.8513 (p0) REVERT: A 37 ILE cc_start: 0.8885 (mm) cc_final: 0.8571 (mm) REVERT: A 51 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8649 (pp) REVERT: A 70 MET cc_start: 0.8430 (mpp) cc_final: 0.8124 (mpp) REVERT: A 105 ARG cc_start: 0.8558 (ttp-110) cc_final: 0.8318 (ttp-110) REVERT: A 168 GLU cc_start: 0.8806 (mp0) cc_final: 0.8391 (pm20) REVERT: A 175 LEU cc_start: 0.9545 (mp) cc_final: 0.9249 (mp) REVERT: A 179 MET cc_start: 0.8698 (ptt) cc_final: 0.8329 (ptt) REVERT: A 216 ASP cc_start: 0.9107 (t70) cc_final: 0.8580 (t0) REVERT: A 272 VAL cc_start: 0.8941 (t) cc_final: 0.8534 (p) REVERT: A 325 MET cc_start: 0.8619 (ttm) cc_final: 0.8403 (ttp) REVERT: A 330 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9050 (pp) REVERT: A 352 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8618 (tm-30) REVERT: A 355 ARG cc_start: 0.9052 (ptt90) cc_final: 0.8551 (ttp-170) REVERT: A 364 ASP cc_start: 0.9246 (OUTLIER) cc_final: 0.8799 (t70) REVERT: A 385 MET cc_start: 0.9249 (ttm) cc_final: 0.8920 (ttp) REVERT: A 399 GLU cc_start: 0.6814 (tm-30) cc_final: 0.6507 (tp30) REVERT: A 400 TYR cc_start: 0.8697 (m-80) cc_final: 0.8279 (m-80) REVERT: A 410 LYS cc_start: 0.7912 (pttt) cc_final: 0.7178 (mtpp) REVERT: A 512 ARG cc_start: 0.8298 (ttp-170) cc_final: 0.7827 (mtp85) REVERT: I 1 MET cc_start: 0.5737 (OUTLIER) cc_final: 0.2942 (pp-130) REVERT: B 34 ASP cc_start: 0.8819 (p0) cc_final: 0.8609 (p0) REVERT: B 37 ILE cc_start: 0.8734 (mm) cc_final: 0.8356 (mm) REVERT: B 43 ASP cc_start: 0.8895 (p0) cc_final: 0.8658 (p0) REVERT: B 51 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8672 (pp) REVERT: B 70 MET cc_start: 0.8443 (mpp) cc_final: 0.8098 (mpp) REVERT: B 105 ARG cc_start: 0.8385 (ttp-110) cc_final: 0.8181 (ttp-110) REVERT: B 168 GLU cc_start: 0.8736 (mp0) cc_final: 0.8377 (pm20) REVERT: B 175 LEU cc_start: 0.9513 (mp) cc_final: 0.9194 (mp) REVERT: B 179 MET cc_start: 0.8601 (ptt) cc_final: 0.8294 (ptt) REVERT: B 202 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: B 216 ASP cc_start: 0.8947 (t70) cc_final: 0.8467 (t0) REVERT: B 258 TYR cc_start: 0.8773 (t80) cc_final: 0.8442 (t80) REVERT: B 272 VAL cc_start: 0.8815 (t) cc_final: 0.8389 (p) REVERT: B 279 ASN cc_start: 0.8215 (t0) cc_final: 0.7504 (t0) REVERT: B 330 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.8923 (pp) REVERT: B 352 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8706 (tm-30) REVERT: B 355 ARG cc_start: 0.9083 (ptt90) cc_final: 0.8636 (ttp-170) REVERT: B 364 ASP cc_start: 0.9333 (OUTLIER) cc_final: 0.8758 (t70) REVERT: B 385 MET cc_start: 0.9203 (ttm) cc_final: 0.8982 (ttm) REVERT: B 411 TYR cc_start: 0.8963 (t80) cc_final: 0.8103 (t80) REVERT: C 15 ASP cc_start: 0.8556 (t0) cc_final: 0.8115 (t70) REVERT: C 16 ASP cc_start: 0.8567 (t0) cc_final: 0.8293 (t0) REVERT: C 34 ASP cc_start: 0.8864 (p0) cc_final: 0.8650 (p0) REVERT: C 37 ILE cc_start: 0.8957 (mm) cc_final: 0.8639 (mm) REVERT: C 43 ASP cc_start: 0.8898 (p0) cc_final: 0.8691 (p0) REVERT: C 70 MET cc_start: 0.8431 (mpp) cc_final: 0.7982 (mpp) REVERT: C 105 ARG cc_start: 0.8539 (ttp-110) cc_final: 0.8300 (ttp-110) REVERT: C 168 GLU cc_start: 0.8843 (mp0) cc_final: 0.8381 (pm20) REVERT: C 179 MET cc_start: 0.8582 (ptt) cc_final: 0.8196 (ptt) REVERT: C 202 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: C 205 LYS cc_start: 0.9228 (mptm) cc_final: 0.8775 (mptt) REVERT: C 258 TYR cc_start: 0.8697 (t80) cc_final: 0.8286 (t80) REVERT: C 272 VAL cc_start: 0.8983 (t) cc_final: 0.8488 (p) REVERT: C 330 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9000 (pp) REVERT: C 352 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8576 (tm-30) REVERT: C 364 ASP cc_start: 0.9245 (OUTLIER) cc_final: 0.8957 (t70) REVERT: C 385 MET cc_start: 0.9254 (ttm) cc_final: 0.8822 (ttm) REVERT: C 411 TYR cc_start: 0.9022 (t80) cc_final: 0.8228 (t80) REVERT: K 1 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.2874 (pp-130) REVERT: D 43 ASP cc_start: 0.8908 (p0) cc_final: 0.8658 (p0) REVERT: D 51 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8640 (pp) REVERT: D 70 MET cc_start: 0.8374 (mpp) cc_final: 0.8031 (mpp) REVERT: D 164 ASP cc_start: 0.8112 (t70) cc_final: 0.7834 (t70) REVERT: D 168 GLU cc_start: 0.8759 (mp0) cc_final: 0.8328 (pm20) REVERT: D 175 LEU cc_start: 0.9543 (mp) cc_final: 0.9237 (mp) REVERT: D 179 MET cc_start: 0.8720 (ptt) cc_final: 0.8385 (ptt) REVERT: D 202 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: D 205 LYS cc_start: 0.9312 (mptm) cc_final: 0.8829 (mptt) REVERT: D 216 ASP cc_start: 0.9010 (t70) cc_final: 0.8539 (t0) REVERT: D 250 ILE cc_start: 0.8591 (pp) cc_final: 0.8351 (pp) REVERT: D 269 ASP cc_start: 0.8331 (m-30) cc_final: 0.8089 (m-30) REVERT: D 274 ASP cc_start: 0.8784 (t0) cc_final: 0.8584 (t0) REVERT: D 279 ASN cc_start: 0.8168 (t0) cc_final: 0.7382 (t0) REVERT: D 330 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.8933 (pp) REVERT: D 352 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8633 (tm-30) REVERT: D 364 ASP cc_start: 0.9338 (OUTLIER) cc_final: 0.8565 (t70) REVERT: D 385 MET cc_start: 0.9207 (ttm) cc_final: 0.8853 (ttp) REVERT: D 394 THR cc_start: 0.9351 (p) cc_final: 0.9056 (p) REVERT: D 411 TYR cc_start: 0.8954 (t80) cc_final: 0.8178 (t80) REVERT: L 1 MET cc_start: 0.5581 (OUTLIER) cc_final: 0.4861 (pmm) REVERT: E 37 ILE cc_start: 0.8835 (mm) cc_final: 0.8479 (mm) REVERT: E 43 ASP cc_start: 0.8874 (p0) cc_final: 0.8666 (p0) REVERT: E 51 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8698 (pp) REVERT: E 70 MET cc_start: 0.8444 (mpp) cc_final: 0.7952 (mpp) REVERT: E 168 GLU cc_start: 0.8713 (mp0) cc_final: 0.8362 (pm20) REVERT: E 179 MET cc_start: 0.8555 (ptt) cc_final: 0.8244 (ptt) REVERT: E 216 ASP cc_start: 0.9046 (t70) cc_final: 0.8523 (t0) REVERT: E 258 TYR cc_start: 0.8593 (t80) cc_final: 0.8215 (t80) REVERT: E 272 VAL cc_start: 0.8956 (t) cc_final: 0.8545 (p) REVERT: E 325 MET cc_start: 0.8771 (ttm) cc_final: 0.8504 (ttp) REVERT: E 330 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9043 (pp) REVERT: E 352 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8590 (tm-30) REVERT: E 364 ASP cc_start: 0.9257 (OUTLIER) cc_final: 0.8877 (t70) REVERT: E 394 THR cc_start: 0.9361 (p) cc_final: 0.9061 (p) REVERT: E 411 TYR cc_start: 0.9033 (t80) cc_final: 0.8215 (t80) REVERT: F 37 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8542 (mm) REVERT: F 43 ASP cc_start: 0.8910 (p0) cc_final: 0.8651 (p0) REVERT: F 51 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8628 (pp) REVERT: F 70 MET cc_start: 0.8369 (mpp) cc_final: 0.8022 (mpp) REVERT: F 75 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7620 (mp0) REVERT: F 78 MET cc_start: 0.9080 (ttp) cc_final: 0.8758 (ttp) REVERT: F 82 MET cc_start: 0.9409 (mmm) cc_final: 0.9125 (mmm) REVERT: F 168 GLU cc_start: 0.8745 (mp0) cc_final: 0.8401 (pm20) REVERT: F 175 LEU cc_start: 0.9481 (mp) cc_final: 0.9158 (mp) REVERT: F 179 MET cc_start: 0.8639 (ptt) cc_final: 0.8331 (ptt) REVERT: F 216 ASP cc_start: 0.8899 (t70) cc_final: 0.8448 (t0) REVERT: F 272 VAL cc_start: 0.8766 (t) cc_final: 0.8358 (p) REVERT: F 330 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.8925 (pp) REVERT: F 352 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8638 (tm-30) REVERT: F 364 ASP cc_start: 0.9302 (OUTLIER) cc_final: 0.8762 (t70) REVERT: F 411 TYR cc_start: 0.8962 (t80) cc_final: 0.8281 (t80) REVERT: F 505 SER cc_start: 0.9023 (t) cc_final: 0.8665 (t) REVERT: N 1 MET cc_start: 0.5887 (OUTLIER) cc_final: 0.2797 (pp-130) REVERT: G 43 ASP cc_start: 0.8888 (p0) cc_final: 0.8664 (p0) REVERT: G 51 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8700 (pp) REVERT: G 70 MET cc_start: 0.8353 (mpp) cc_final: 0.7933 (mpp) REVERT: G 82 MET cc_start: 0.9434 (mmm) cc_final: 0.9199 (mmm) REVERT: G 168 GLU cc_start: 0.8741 (mp0) cc_final: 0.8414 (pm20) REVERT: G 175 LEU cc_start: 0.9553 (mp) cc_final: 0.9285 (mp) REVERT: G 179 MET cc_start: 0.8649 (ptt) cc_final: 0.8326 (ptt) REVERT: G 259 ARG cc_start: 0.8394 (mtp85) cc_final: 0.8175 (ttm110) REVERT: G 262 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8736 (tp) REVERT: G 265 GLN cc_start: 0.9264 (mm110) cc_final: 0.9034 (mp10) REVERT: G 272 VAL cc_start: 0.8942 (t) cc_final: 0.8524 (p) REVERT: G 330 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.9037 (pp) REVERT: G 352 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8632 (tm-30) REVERT: G 364 ASP cc_start: 0.9257 (OUTLIER) cc_final: 0.8775 (t70) REVERT: G 385 MET cc_start: 0.9258 (ttm) cc_final: 0.8916 (ttp) REVERT: G 394 THR cc_start: 0.9370 (p) cc_final: 0.9118 (p) REVERT: G 411 TYR cc_start: 0.9007 (t80) cc_final: 0.8196 (t80) REVERT: O 1 MET cc_start: 0.5594 (OUTLIER) cc_final: 0.5146 (pmm) REVERT: H 37 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8573 (mm) REVERT: H 43 ASP cc_start: 0.8881 (p0) cc_final: 0.8650 (p0) REVERT: H 51 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8568 (pp) REVERT: H 70 MET cc_start: 0.8431 (mpp) cc_final: 0.7704 (mtp) REVERT: H 75 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7659 (mp0) REVERT: H 78 MET cc_start: 0.9088 (ttp) cc_final: 0.8774 (ttp) REVERT: H 82 MET cc_start: 0.9415 (mmm) cc_final: 0.9171 (tpp) REVERT: H 128 ARG cc_start: 0.8158 (ptt-90) cc_final: 0.7829 (ptt-90) REVERT: H 168 GLU cc_start: 0.8734 (mp0) cc_final: 0.8380 (pm20) REVERT: H 175 LEU cc_start: 0.9553 (mp) cc_final: 0.9251 (mp) REVERT: H 179 MET cc_start: 0.8705 (ptt) cc_final: 0.8404 (ptt) REVERT: H 216 ASP cc_start: 0.8960 (t70) cc_final: 0.8515 (t0) REVERT: H 253 HIS cc_start: 0.7531 (m-70) cc_final: 0.7321 (m-70) REVERT: H 265 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8618 (mm-40) REVERT: H 279 ASN cc_start: 0.8291 (t0) cc_final: 0.7534 (t0) REVERT: H 330 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.8924 (pp) REVERT: H 352 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8615 (tm-30) REVERT: H 364 ASP cc_start: 0.9344 (OUTLIER) cc_final: 0.8757 (t70) REVERT: H 385 MET cc_start: 0.9213 (ttm) cc_final: 0.8751 (ttm) REVERT: H 411 TYR cc_start: 0.8944 (t80) cc_final: 0.8329 (t80) REVERT: H 505 SER cc_start: 0.8956 (t) cc_final: 0.8655 (t) REVERT: P 1 MET cc_start: 0.5851 (OUTLIER) cc_final: 0.2723 (pp-130) outliers start: 210 outliers final: 81 residues processed: 1251 average time/residue: 0.1794 time to fit residues: 368.7559 Evaluate side-chains 1050 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 933 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 466 HIS Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 410 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 466 HIS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 265 GLN Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 466 HIS Chi-restraints excluded: chain P residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 201 optimal weight: 0.0980 chunk 174 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 171 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 chunk 292 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 302 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN A 334 GLN B 94 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN B 334 GLN C 94 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN C 343 GLN D 94 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN D 334 GLN E 94 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN F 94 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN F 334 GLN G 94 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 GLN G 334 GLN H 94 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 GLN H 334 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103778 restraints weight = 50522.174| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.40 r_work: 0.3052 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32360 Z= 0.144 Angle : 0.714 8.769 43936 Z= 0.340 Chirality : 0.048 0.184 5000 Planarity : 0.004 0.039 5456 Dihedral : 16.035 165.613 4738 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 6.23 % Allowed : 22.31 % Favored : 71.45 % 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: -2.08 (0.13), residues: 3968 helix: -0.88 (0.13), residues: 1312 sheet: -1.54 (0.24), residues: 432 loop : -1.66 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 126 TYR 0.016 0.001 TYR A 258 PHE 0.018 0.001 PHE B 165 HIS 0.003 0.001 HIS C 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (32352) covalent geometry : angle 0.71441 / 0.34 (43936) hydrogen bonds : bond 0.03674 / 2.40 ( 992) hydrogen bonds : angle 5.35641 / 3.67 ( 2832) Misc. bond : bond 0.00076 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 992 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8373 (t0) cc_final: 0.8154 (t0) REVERT: A 37 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8542 (mm) REVERT: A 51 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8706 (pp) REVERT: A 70 MET cc_start: 0.8603 (mpp) cc_final: 0.8293 (mpp) REVERT: A 78 MET cc_start: 0.8854 (ttp) cc_final: 0.8645 (tmm) REVERT: A 111 GLU cc_start: 0.9277 (mm-30) cc_final: 0.9057 (mm-30) REVERT: A 136 ARG cc_start: 0.8985 (ttm110) cc_final: 0.8609 (mtp-110) REVERT: A 150 MET cc_start: 0.8441 (tmm) cc_final: 0.7998 (tmm) REVERT: A 168 GLU cc_start: 0.8848 (mp0) cc_final: 0.8427 (pm20) REVERT: A 175 LEU cc_start: 0.9575 (mp) cc_final: 0.9340 (mp) REVERT: A 179 MET cc_start: 0.8690 (ptt) cc_final: 0.8425 (ptt) REVERT: A 185 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8602 (mt) REVERT: A 253 HIS cc_start: 0.7569 (m-70) cc_final: 0.7316 (m-70) REVERT: A 258 TYR cc_start: 0.8669 (t80) cc_final: 0.8313 (t80) REVERT: A 272 VAL cc_start: 0.8837 (t) cc_final: 0.8474 (p) REVERT: A 274 ASP cc_start: 0.8937 (t0) cc_final: 0.8734 (t0) REVERT: A 330 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9046 (pp) REVERT: A 352 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8685 (tm-30) REVERT: A 364 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8884 (t70) REVERT: A 385 MET cc_start: 0.9300 (ttm) cc_final: 0.9003 (ttp) REVERT: A 400 TYR cc_start: 0.8821 (m-80) cc_final: 0.8300 (m-80) REVERT: A 410 LYS cc_start: 0.8025 (pttt) cc_final: 0.7706 (pttp) REVERT: I 1 MET cc_start: 0.5874 (OUTLIER) cc_final: 0.2907 (pp-130) REVERT: B 48 GLN cc_start: 0.9056 (tt0) cc_final: 0.8715 (mt0) REVERT: B 51 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8815 (pp) REVERT: B 70 MET cc_start: 0.8553 (mpp) cc_final: 0.8246 (mpp) REVERT: B 78 MET cc_start: 0.8984 (ttp) cc_final: 0.8748 (ttp) REVERT: B 98 GLU cc_start: 0.9233 (mp0) cc_final: 0.8764 (mp0) REVERT: B 121 LEU cc_start: 0.8382 (mp) cc_final: 0.8156 (mt) REVERT: B 136 ARG cc_start: 0.8950 (ttm110) cc_final: 0.8619 (mtp-110) REVERT: B 168 GLU cc_start: 0.8879 (mp0) cc_final: 0.8444 (pm20) REVERT: B 175 LEU cc_start: 0.9529 (mp) cc_final: 0.9216 (mp) REVERT: B 179 MET cc_start: 0.8633 (ptt) cc_final: 0.8417 (ptt) REVERT: B 232 ASP cc_start: 0.8906 (m-30) cc_final: 0.8470 (t0) REVERT: B 253 HIS cc_start: 0.7769 (m-70) cc_final: 0.7568 (m-70) REVERT: B 258 TYR cc_start: 0.8787 (t80) cc_final: 0.8207 (t80) REVERT: B 272 VAL cc_start: 0.8656 (t) cc_final: 0.8300 (p) REVERT: B 274 ASP cc_start: 0.8918 (t0) cc_final: 0.8709 (t0) REVERT: B 330 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.8939 (pp) REVERT: B 352 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8763 (tm-30) REVERT: B 364 ASP cc_start: 0.9234 (OUTLIER) cc_final: 0.8985 (t70) REVERT: B 385 MET cc_start: 0.9257 (ttm) cc_final: 0.8977 (ttp) REVERT: B 414 MET cc_start: 0.9192 (mmm) cc_final: 0.8914 (mmm) REVERT: C 15 ASP cc_start: 0.8632 (t0) cc_final: 0.8258 (t0) REVERT: C 70 MET cc_start: 0.8617 (mpp) cc_final: 0.8327 (mpp) REVERT: C 78 MET cc_start: 0.8831 (ttp) cc_final: 0.8596 (tmm) REVERT: C 105 ARG cc_start: 0.8552 (ttp-110) cc_final: 0.8332 (ttp-110) REVERT: C 136 ARG cc_start: 0.8948 (ttm110) cc_final: 0.8567 (mtp-110) REVERT: C 168 GLU cc_start: 0.8738 (mp0) cc_final: 0.8301 (pm20) REVERT: C 179 MET cc_start: 0.8636 (ptt) cc_final: 0.8342 (ptt) REVERT: C 202 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: C 253 HIS cc_start: 0.7611 (m-70) cc_final: 0.7335 (m-70) REVERT: C 254 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8620 (tm-30) REVERT: C 258 TYR cc_start: 0.8634 (t80) cc_final: 0.8327 (t80) REVERT: C 272 VAL cc_start: 0.8860 (t) cc_final: 0.8445 (p) REVERT: C 330 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9053 (pp) REVERT: C 352 GLU cc_start: 0.9258 (tm-30) cc_final: 0.8838 (tm-30) REVERT: C 355 ARG cc_start: 0.9018 (ptt90) cc_final: 0.8633 (ttp-170) REVERT: C 399 GLU cc_start: 0.7565 (tp30) cc_final: 0.7312 (tp30) REVERT: C 512 ARG cc_start: 0.8236 (mtp180) cc_final: 0.7943 (mmm-85) REVERT: K 1 MET cc_start: 0.5919 (OUTLIER) cc_final: 0.2766 (pp-130) REVERT: D 37 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8268 (mm) REVERT: D 51 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8693 (pp) REVERT: D 70 MET cc_start: 0.8666 (mpp) cc_final: 0.8316 (mpp) REVERT: D 136 ARG cc_start: 0.8931 (ttm110) cc_final: 0.8599 (mtp-110) REVERT: D 150 MET cc_start: 0.8514 (tmm) cc_final: 0.8018 (tmm) REVERT: D 168 GLU cc_start: 0.8864 (mp0) cc_final: 0.8366 (pm20) REVERT: D 175 LEU cc_start: 0.9591 (mp) cc_final: 0.9283 (mp) REVERT: D 179 MET cc_start: 0.8779 (ptt) cc_final: 0.8528 (ptt) REVERT: D 226 ASP cc_start: 0.8964 (m-30) cc_final: 0.8756 (m-30) REVERT: D 232 ASP cc_start: 0.8995 (m-30) cc_final: 0.8509 (t0) REVERT: D 254 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8604 (tm-30) REVERT: D 330 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.8956 (pp) REVERT: D 352 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8769 (tm-30) REVERT: D 364 ASP cc_start: 0.9259 (OUTLIER) cc_final: 0.8876 (t70) REVERT: D 385 MET cc_start: 0.9249 (ttm) cc_final: 0.8946 (ttp) REVERT: D 399 GLU cc_start: 0.7637 (tp30) cc_final: 0.7405 (tp30) REVERT: L 1 MET cc_start: 0.5580 (OUTLIER) cc_final: 0.2596 (pp-130) REVERT: E 16 ASP cc_start: 0.8384 (t0) cc_final: 0.8123 (t0) REVERT: E 37 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8508 (mm) REVERT: E 51 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8858 (pp) REVERT: E 70 MET cc_start: 0.8625 (mpp) cc_final: 0.8254 (mpp) REVERT: E 136 ARG cc_start: 0.8929 (ttm110) cc_final: 0.8556 (mtp-110) REVERT: E 168 GLU cc_start: 0.8818 (mp0) cc_final: 0.8410 (pm20) REVERT: E 226 ASP cc_start: 0.8907 (m-30) cc_final: 0.8704 (m-30) REVERT: E 232 ASP cc_start: 0.9120 (m-30) cc_final: 0.8492 (t0) REVERT: E 253 HIS cc_start: 0.7730 (m-70) cc_final: 0.7488 (m-70) REVERT: E 254 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8637 (tm-30) REVERT: E 258 TYR cc_start: 0.8668 (t80) cc_final: 0.8370 (t80) REVERT: E 272 VAL cc_start: 0.8838 (t) cc_final: 0.8471 (p) REVERT: E 325 MET cc_start: 0.8846 (ttm) cc_final: 0.8554 (ttp) REVERT: E 330 ILE cc_start: 0.9499 (OUTLIER) cc_final: 0.9108 (pp) REVERT: E 352 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8836 (tm-30) REVERT: E 355 ARG cc_start: 0.9032 (ptt90) cc_final: 0.8813 (ttp-170) REVERT: F 37 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8445 (mm) REVERT: F 51 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8897 (pp) REVERT: F 70 MET cc_start: 0.8548 (mpp) cc_final: 0.7864 (mtp) REVERT: F 128 ARG cc_start: 0.8685 (mmm-85) cc_final: 0.8422 (mtm-85) REVERT: F 136 ARG cc_start: 0.8881 (ttm110) cc_final: 0.8565 (mtp-110) REVERT: F 150 MET cc_start: 0.8606 (tmm) cc_final: 0.8256 (tmm) REVERT: F 168 GLU cc_start: 0.8821 (mp0) cc_final: 0.8382 (pm20) REVERT: F 175 LEU cc_start: 0.9526 (mp) cc_final: 0.9191 (mp) REVERT: F 179 MET cc_start: 0.8716 (ptt) cc_final: 0.8470 (ptt) REVERT: F 226 ASP cc_start: 0.8936 (m-30) cc_final: 0.8719 (m-30) REVERT: F 232 ASP cc_start: 0.8954 (m-30) cc_final: 0.8493 (t0) REVERT: F 253 HIS cc_start: 0.7754 (m-70) cc_final: 0.7548 (m-70) REVERT: F 258 TYR cc_start: 0.8636 (t80) cc_final: 0.8050 (t80) REVERT: F 330 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.8950 (pp) REVERT: F 352 GLU cc_start: 0.9216 (tm-30) cc_final: 0.8744 (tm-30) REVERT: F 385 MET cc_start: 0.9245 (ttm) cc_final: 0.9041 (ttp) REVERT: F 480 ARG cc_start: 0.9333 (mtm110) cc_final: 0.8980 (mtm-85) REVERT: F 505 SER cc_start: 0.8996 (t) cc_final: 0.8690 (t) REVERT: N 1 MET cc_start: 0.5602 (OUTLIER) cc_final: 0.2440 (pp-130) REVERT: G 16 ASP cc_start: 0.8430 (t0) cc_final: 0.8191 (t0) REVERT: G 37 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8489 (mm) REVERT: G 51 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8781 (pp) REVERT: G 70 MET cc_start: 0.8559 (mpp) cc_final: 0.8299 (mpp) REVERT: G 112 GLN cc_start: 0.8667 (mm110) cc_final: 0.8395 (mm110) REVERT: G 136 ARG cc_start: 0.8896 (ttm110) cc_final: 0.8544 (mtp-110) REVERT: G 150 MET cc_start: 0.8493 (tmm) cc_final: 0.8096 (tmm) REVERT: G 168 GLU cc_start: 0.8871 (mp0) cc_final: 0.8484 (pm20) REVERT: G 175 LEU cc_start: 0.9600 (mp) cc_final: 0.9326 (mp) REVERT: G 179 MET cc_start: 0.8729 (ptt) cc_final: 0.8437 (ptt) REVERT: G 202 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8357 (tt0) REVERT: G 226 ASP cc_start: 0.8881 (m-30) cc_final: 0.8633 (m-30) REVERT: G 253 HIS cc_start: 0.7531 (m-70) cc_final: 0.7269 (m-70) REVERT: G 258 TYR cc_start: 0.8747 (t80) cc_final: 0.8165 (t80) REVERT: G 272 VAL cc_start: 0.8847 (t) cc_final: 0.8473 (p) REVERT: G 330 ILE cc_start: 0.9499 (OUTLIER) cc_final: 0.9097 (pp) REVERT: G 352 GLU cc_start: 0.9271 (tm-30) cc_final: 0.8771 (tm-30) REVERT: G 414 MET cc_start: 0.9145 (mmm) cc_final: 0.8936 (mmm) REVERT: O 1 MET cc_start: 0.5915 (OUTLIER) cc_final: 0.5168 (pmm) REVERT: H 37 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8403 (mm) REVERT: H 51 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8811 (pp) REVERT: H 70 MET cc_start: 0.8556 (mpp) cc_final: 0.7876 (mtp) REVERT: H 78 MET cc_start: 0.8836 (ttp) cc_final: 0.8494 (tmm) REVERT: H 136 ARG cc_start: 0.8956 (ttm110) cc_final: 0.8599 (mtp-110) REVERT: H 150 MET cc_start: 0.8546 (tmm) cc_final: 0.8215 (tmm) REVERT: H 164 ASP cc_start: 0.8291 (t0) cc_final: 0.7892 (t0) REVERT: H 168 GLU cc_start: 0.8829 (mp0) cc_final: 0.8409 (pm20) REVERT: H 175 LEU cc_start: 0.9608 (mp) cc_final: 0.9312 (mp) REVERT: H 179 MET cc_start: 0.8768 (ptt) cc_final: 0.8539 (ptt) REVERT: H 202 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8790 (tt0) REVERT: H 232 ASP cc_start: 0.8953 (m-30) cc_final: 0.8541 (t0) REVERT: H 253 HIS cc_start: 0.7634 (m-70) cc_final: 0.7390 (m-70) REVERT: H 330 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8916 (pp) REVERT: H 352 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8720 (tm-30) REVERT: H 395 GLU cc_start: 0.8762 (mp0) cc_final: 0.8431 (mp0) REVERT: H 400 TYR cc_start: 0.8668 (m-80) cc_final: 0.8034 (m-10) REVERT: H 505 SER cc_start: 0.8994 (t) cc_final: 0.8704 (t) REVERT: P 1 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.2696 (pp-130) outliers start: 204 outliers final: 100 residues processed: 1087 average time/residue: 0.1831 time to fit residues: 327.1259 Evaluate side-chains 1052 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 918 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 466 HIS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 466 HIS Chi-restraints excluded: chain P residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 220 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 190 optimal weight: 0.6980 chunk 225 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 365 optimal weight: 0.6980 chunk 377 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 342 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 HIS B 93 HIS B 202 GLN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS C 94 ASN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS F 93 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS H 93 HIS ** H 277 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 = 0.3675 r_free = 0.3675 target = 0.137697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103222 restraints weight = 50965.592| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.48 r_work: 0.3066 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32360 Z= 0.142 Angle : 0.705 8.397 43936 Z= 0.331 Chirality : 0.048 0.181 5000 Planarity : 0.004 0.045 5456 Dihedral : 15.636 166.900 4722 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 7.27 % Allowed : 22.98 % Favored : 69.74 % 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: -1.76 (0.13), residues: 3968 helix: -0.48 (0.14), residues: 1320 sheet: -1.31 (0.23), residues: 520 loop : -1.57 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 128 TYR 0.014 0.001 TYR H 353 PHE 0.017 0.001 PHE B 401 HIS 0.003 0.001 HIS F 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (32352) covalent geometry : angle 0.70502 / 0.33 (43936) hydrogen bonds : bond 0.03365 / 2.21 ( 992) hydrogen bonds : angle 5.18712 / 3.53 ( 2832) Misc. bond : bond 0.00074 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 1011 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8357 (mm) REVERT: A 51 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8790 (pp) REVERT: A 70 MET cc_start: 0.8672 (mpp) cc_final: 0.7888 (mpp) REVERT: A 136 ARG cc_start: 0.8980 (ttm110) cc_final: 0.8630 (mtp-110) REVERT: A 168 GLU cc_start: 0.8904 (mp0) cc_final: 0.8396 (pm20) REVERT: A 175 LEU cc_start: 0.9614 (mp) cc_final: 0.9260 (mp) REVERT: A 179 MET cc_start: 0.8742 (ptt) cc_final: 0.8358 (ptt) REVERT: A 216 ASP cc_start: 0.9026 (OUTLIER) cc_final: 0.8645 (t0) REVERT: A 253 HIS cc_start: 0.7584 (m-70) cc_final: 0.7284 (m-70) REVERT: A 254 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8673 (tm-30) REVERT: A 258 TYR cc_start: 0.8600 (t80) cc_final: 0.8347 (t80) REVERT: A 272 VAL cc_start: 0.8863 (t) cc_final: 0.8522 (p) REVERT: A 274 ASP cc_start: 0.8882 (t0) cc_final: 0.8679 (t0) REVERT: A 330 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9045 (pp) REVERT: A 352 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8798 (tm-30) REVERT: A 355 ARG cc_start: 0.8978 (ptt90) cc_final: 0.8688 (ttp-170) REVERT: A 385 MET cc_start: 0.9221 (ttm) cc_final: 0.9003 (ttm) REVERT: A 393 THR cc_start: 0.8414 (p) cc_final: 0.7591 (t) REVERT: A 395 GLU cc_start: 0.8841 (mp0) cc_final: 0.8494 (mp0) REVERT: A 410 LYS cc_start: 0.8028 (pttt) cc_final: 0.7721 (pttp) REVERT: A 512 ARG cc_start: 0.8342 (ttp80) cc_final: 0.7679 (mtp85) REVERT: I 1 MET cc_start: 0.5857 (OUTLIER) cc_final: 0.2917 (pp-130) REVERT: B 37 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8205 (mm) REVERT: B 48 GLN cc_start: 0.9041 (tt0) cc_final: 0.8747 (mt0) REVERT: B 51 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8841 (pp) REVERT: B 78 MET cc_start: 0.9075 (ttp) cc_final: 0.8812 (ttp) REVERT: B 82 MET cc_start: 0.9381 (mmm) cc_final: 0.9146 (mmm) REVERT: B 98 GLU cc_start: 0.9205 (mp0) cc_final: 0.8804 (mp0) REVERT: B 128 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7519 (mtm110) REVERT: B 168 GLU cc_start: 0.8961 (mp0) cc_final: 0.8526 (pm20) REVERT: B 175 LEU cc_start: 0.9371 (mp) cc_final: 0.8964 (mp) REVERT: B 179 MET cc_start: 0.8647 (ptt) cc_final: 0.8367 (ptt) REVERT: B 224 ARG cc_start: 0.8881 (ptm160) cc_final: 0.8617 (ptm160) REVERT: B 232 ASP cc_start: 0.8903 (m-30) cc_final: 0.8508 (t0) REVERT: B 253 HIS cc_start: 0.7802 (m-70) cc_final: 0.7602 (m-70) REVERT: B 258 TYR cc_start: 0.8741 (t80) cc_final: 0.8493 (t80) REVERT: B 272 VAL cc_start: 0.8732 (t) cc_final: 0.8393 (p) REVERT: B 330 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.8953 (pp) REVERT: B 385 MET cc_start: 0.9219 (ttm) cc_final: 0.8995 (ttp) REVERT: C 37 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8395 (mm) REVERT: C 70 MET cc_start: 0.8675 (mpp) cc_final: 0.7793 (mtp) REVERT: C 98 GLU cc_start: 0.9149 (mp0) cc_final: 0.8467 (mp0) REVERT: C 105 ARG cc_start: 0.8532 (ttp-110) cc_final: 0.8330 (ttp-110) REVERT: C 136 ARG cc_start: 0.8936 (ttm110) cc_final: 0.8588 (mtp-110) REVERT: C 168 GLU cc_start: 0.8813 (mp0) cc_final: 0.8402 (pm20) REVERT: C 179 MET cc_start: 0.8646 (ptt) cc_final: 0.8268 (ptt) REVERT: C 202 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8637 (mt0) REVERT: C 253 HIS cc_start: 0.7600 (m-70) cc_final: 0.7324 (m-70) REVERT: C 254 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8649 (tm-30) REVERT: C 258 TYR cc_start: 0.8592 (t80) cc_final: 0.8319 (t80) REVERT: C 272 VAL cc_start: 0.8870 (t) cc_final: 0.8527 (p) REVERT: C 330 ILE cc_start: 0.9486 (OUTLIER) cc_final: 0.9098 (pp) REVERT: C 352 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8771 (tm-30) REVERT: C 385 MET cc_start: 0.9226 (ttm) cc_final: 0.8902 (ttp) REVERT: C 399 GLU cc_start: 0.7745 (tp30) cc_final: 0.7449 (tp30) REVERT: C 512 ARG cc_start: 0.8339 (mtp180) cc_final: 0.8055 (mmm-85) REVERT: K 1 MET cc_start: 0.5995 (OUTLIER) cc_final: 0.2905 (pp-130) REVERT: D 37 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8201 (mm) REVERT: D 51 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8772 (pp) REVERT: D 70 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8294 (mtp) REVERT: D 98 GLU cc_start: 0.9072 (mp0) cc_final: 0.8433 (mp0) REVERT: D 121 LEU cc_start: 0.8444 (mp) cc_final: 0.8230 (mt) REVERT: D 136 ARG cc_start: 0.8925 (ttm110) cc_final: 0.8594 (mtp-110) REVERT: D 168 GLU cc_start: 0.8918 (mp0) cc_final: 0.8455 (pm20) REVERT: D 175 LEU cc_start: 0.9592 (mp) cc_final: 0.9198 (mp) REVERT: D 179 MET cc_start: 0.8776 (ptt) cc_final: 0.8430 (ptt) REVERT: D 226 ASP cc_start: 0.8970 (m-30) cc_final: 0.8726 (m-30) REVERT: D 330 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.8967 (pp) REVERT: D 379 LEU cc_start: 0.9344 (mm) cc_final: 0.8984 (mt) REVERT: D 385 MET cc_start: 0.9251 (ttm) cc_final: 0.9008 (ttp) REVERT: D 393 THR cc_start: 0.8533 (p) cc_final: 0.8152 (p) REVERT: D 395 GLU cc_start: 0.8784 (mp0) cc_final: 0.8556 (mp0) REVERT: D 399 GLU cc_start: 0.7790 (tp30) cc_final: 0.7539 (tp30) REVERT: L 1 MET cc_start: 0.5592 (OUTLIER) cc_final: 0.2484 (pp-130) REVERT: E 16 ASP cc_start: 0.8486 (t0) cc_final: 0.8178 (t0) REVERT: E 28 ASP cc_start: 0.8862 (p0) cc_final: 0.8523 (p0) REVERT: E 37 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8341 (mm) REVERT: E 51 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8872 (pp) REVERT: E 59 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8767 (pt) REVERT: E 70 MET cc_start: 0.8654 (mpp) cc_final: 0.8157 (mpp) REVERT: E 98 GLU cc_start: 0.9159 (mp0) cc_final: 0.8504 (mp0) REVERT: E 136 ARG cc_start: 0.8892 (ttm110) cc_final: 0.8534 (mtp-110) REVERT: E 168 GLU cc_start: 0.8876 (mp0) cc_final: 0.8444 (pm20) REVERT: E 175 LEU cc_start: 0.9496 (mp) cc_final: 0.9217 (mp) REVERT: E 226 ASP cc_start: 0.8942 (m-30) cc_final: 0.8742 (m-30) REVERT: E 253 HIS cc_start: 0.7741 (m-70) cc_final: 0.7511 (m-70) REVERT: E 258 TYR cc_start: 0.8650 (t80) cc_final: 0.8177 (t80) REVERT: E 272 VAL cc_start: 0.8908 (t) cc_final: 0.8571 (p) REVERT: E 330 ILE cc_start: 0.9518 (OUTLIER) cc_final: 0.9130 (pp) REVERT: E 352 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8766 (tm-30) REVERT: E 383 THR cc_start: 0.9437 (p) cc_final: 0.9141 (t) REVERT: E 393 THR cc_start: 0.8464 (p) cc_final: 0.7689 (t) REVERT: E 395 GLU cc_start: 0.8755 (mp0) cc_final: 0.8425 (mp0) REVERT: F 37 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8333 (mm) REVERT: F 51 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8972 (pp) REVERT: F 70 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8180 (mtp) REVERT: F 78 MET cc_start: 0.9022 (tmm) cc_final: 0.8655 (ttp) REVERT: F 121 LEU cc_start: 0.8409 (mp) cc_final: 0.8196 (mt) REVERT: F 136 ARG cc_start: 0.8879 (ttm110) cc_final: 0.8528 (mtp-110) REVERT: F 168 GLU cc_start: 0.8847 (mp0) cc_final: 0.8424 (pm20) REVERT: F 175 LEU cc_start: 0.9397 (mp) cc_final: 0.8974 (mp) REVERT: F 179 MET cc_start: 0.8677 (ptt) cc_final: 0.8369 (ptt) REVERT: F 226 ASP cc_start: 0.8934 (m-30) cc_final: 0.8702 (m-30) REVERT: F 253 HIS cc_start: 0.7744 (m-70) cc_final: 0.7520 (m-70) REVERT: F 258 TYR cc_start: 0.8524 (t80) cc_final: 0.7961 (t80) REVERT: F 330 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.8974 (pp) REVERT: F 385 MET cc_start: 0.9231 (ttm) cc_final: 0.8928 (ttp) REVERT: F 480 ARG cc_start: 0.9335 (mtm110) cc_final: 0.9101 (mtm-85) REVERT: N 1 MET cc_start: 0.5685 (OUTLIER) cc_final: 0.2554 (pp-130) REVERT: G 16 ASP cc_start: 0.8586 (t0) cc_final: 0.8344 (t0) REVERT: G 37 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8306 (mm) REVERT: G 51 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8826 (pp) REVERT: G 70 MET cc_start: 0.8566 (mpp) cc_final: 0.7932 (mtp) REVERT: G 112 GLN cc_start: 0.8712 (mm110) cc_final: 0.8393 (mm110) REVERT: G 136 ARG cc_start: 0.8877 (ttm110) cc_final: 0.8520 (mtp-110) REVERT: G 150 MET cc_start: 0.8579 (tmm) cc_final: 0.8226 (tmm) REVERT: G 168 GLU cc_start: 0.8942 (mp0) cc_final: 0.8458 (pm20) REVERT: G 179 MET cc_start: 0.8660 (ptt) cc_final: 0.8322 (ptt) REVERT: G 226 ASP cc_start: 0.8905 (m-30) cc_final: 0.8685 (m-30) REVERT: G 253 HIS cc_start: 0.7558 (m-70) cc_final: 0.7284 (m-70) REVERT: G 254 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8662 (tm-30) REVERT: G 272 VAL cc_start: 0.8832 (t) cc_final: 0.8451 (p) REVERT: G 330 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.9127 (pp) REVERT: G 337 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8291 (tp) REVERT: G 352 GLU cc_start: 0.9257 (tm-30) cc_final: 0.8779 (tm-30) REVERT: O 1 MET cc_start: 0.5887 (OUTLIER) cc_final: 0.4958 (pmm) REVERT: H 37 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8347 (mm) REVERT: H 43 ASP cc_start: 0.9057 (p0) cc_final: 0.8832 (p0) REVERT: H 51 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8872 (pp) REVERT: H 70 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8361 (mtp) REVERT: H 98 GLU cc_start: 0.9150 (mp0) cc_final: 0.8598 (mp0) REVERT: H 128 ARG cc_start: 0.7965 (mtm110) cc_final: 0.7624 (mtm110) REVERT: H 150 MET cc_start: 0.8601 (tmm) cc_final: 0.8271 (tmm) REVERT: H 168 GLU cc_start: 0.8927 (mp0) cc_final: 0.8516 (pm20) REVERT: H 175 LEU cc_start: 0.9456 (mp) cc_final: 0.9064 (mp) REVERT: H 179 MET cc_start: 0.8754 (ptt) cc_final: 0.8462 (ptt) REVERT: H 205 LYS cc_start: 0.9097 (mmtm) cc_final: 0.8886 (mptt) REVERT: H 216 ASP cc_start: 0.9015 (OUTLIER) cc_final: 0.8628 (t0) REVERT: H 232 ASP cc_start: 0.8892 (m-30) cc_final: 0.8480 (t0) REVERT: H 253 HIS cc_start: 0.7588 (m-70) cc_final: 0.7344 (m-70) REVERT: H 330 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.8950 (pp) REVERT: H 352 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8761 (tm-30) REVERT: H 385 MET cc_start: 0.9228 (ttm) cc_final: 0.8979 (ttm) REVERT: H 400 TYR cc_start: 0.8369 (m-80) cc_final: 0.8164 (m-10) REVERT: H 414 MET cc_start: 0.9141 (mmm) cc_final: 0.8904 (mmm) REVERT: H 505 SER cc_start: 0.9012 (t) cc_final: 0.8736 (t) REVERT: P 1 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.2958 (pp-130) outliers start: 238 outliers final: 134 residues processed: 1108 average time/residue: 0.1814 time to fit residues: 332.2581 Evaluate side-chains 1105 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 934 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 265 GLN Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 466 HIS Chi-restraints excluded: chain P residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 290 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 232 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 179 optimal weight: 0.0770 chunk 330 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS B 94 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS E 94 ASN E 334 GLN F 93 HIS ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN H 94 ASN H 202 GLN ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.135456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.100926 restraints weight = 51508.439| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.47 r_work: 0.3017 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32360 Z= 0.143 Angle : 0.699 9.757 43936 Z= 0.329 Chirality : 0.048 0.166 5000 Planarity : 0.004 0.037 5456 Dihedral : 15.420 167.586 4710 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 7.12 % Allowed : 24.02 % Favored : 68.86 % 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: -1.51 (0.13), residues: 3968 helix: -0.21 (0.14), residues: 1312 sheet: -1.40 (0.23), residues: 536 loop : -1.38 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 105 TYR 0.018 0.001 TYR D 258 PHE 0.020 0.001 PHE B 165 HIS 0.004 0.001 HIS H 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (32352) covalent geometry : angle 0.69946 / 0.33 (43936) hydrogen bonds : bond 0.03213 / 2.10 ( 992) hydrogen bonds : angle 5.05972 / 3.45 ( 2832) Misc. bond : bond 0.00064 / 0.04 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 998 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8342 (mm) REVERT: A 51 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8753 (pp) REVERT: A 70 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8194 (mtp) REVERT: A 111 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8958 (mm-30) REVERT: A 112 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7264 (mp10) REVERT: A 136 ARG cc_start: 0.8968 (ttm110) cc_final: 0.8615 (mtp-110) REVERT: A 150 MET cc_start: 0.8502 (tmm) cc_final: 0.7923 (tmm) REVERT: A 168 GLU cc_start: 0.8975 (mp0) cc_final: 0.8550 (pm20) REVERT: A 179 MET cc_start: 0.8709 (ptt) cc_final: 0.8490 (ptm) REVERT: A 205 LYS cc_start: 0.9194 (mmtm) cc_final: 0.8967 (mptt) REVERT: A 216 ASP cc_start: 0.9086 (OUTLIER) cc_final: 0.8683 (t0) REVERT: A 272 VAL cc_start: 0.8859 (t) cc_final: 0.8505 (p) REVERT: A 274 ASP cc_start: 0.8953 (t0) cc_final: 0.8742 (t0) REVERT: A 330 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9012 (pp) REVERT: A 352 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8777 (tm-30) REVERT: A 355 ARG cc_start: 0.8951 (ptt90) cc_final: 0.8704 (ttp-170) REVERT: A 385 MET cc_start: 0.9210 (ttm) cc_final: 0.8892 (ttp) REVERT: A 410 LYS cc_start: 0.7953 (pttt) cc_final: 0.7656 (pttp) REVERT: I 1 MET cc_start: 0.6016 (OUTLIER) cc_final: 0.3169 (pp-130) REVERT: B 37 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8021 (mm) REVERT: B 48 GLN cc_start: 0.9092 (tt0) cc_final: 0.8757 (mt0) REVERT: B 51 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8834 (pp) REVERT: B 78 MET cc_start: 0.9174 (ttp) cc_final: 0.8848 (ttp) REVERT: B 98 GLU cc_start: 0.9238 (mp0) cc_final: 0.8958 (mp0) REVERT: B 168 GLU cc_start: 0.9028 (mp0) cc_final: 0.8682 (pm20) REVERT: B 175 LEU cc_start: 0.9389 (mp) cc_final: 0.8952 (mp) REVERT: B 179 MET cc_start: 0.8765 (ptt) cc_final: 0.8420 (ptt) REVERT: B 224 ARG cc_start: 0.8859 (ptm160) cc_final: 0.8600 (ptm160) REVERT: B 232 ASP cc_start: 0.8891 (m-30) cc_final: 0.8578 (t0) REVERT: B 253 HIS cc_start: 0.7799 (m-70) cc_final: 0.7594 (m-70) REVERT: B 254 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8649 (tm-30) REVERT: B 258 TYR cc_start: 0.8716 (t80) cc_final: 0.8465 (t80) REVERT: B 272 VAL cc_start: 0.8715 (t) cc_final: 0.8373 (p) REVERT: B 330 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8913 (pp) REVERT: B 352 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8606 (tm-30) REVERT: B 385 MET cc_start: 0.9187 (ttm) cc_final: 0.8972 (ttp) REVERT: B 465 GLN cc_start: 0.8649 (pt0) cc_final: 0.8283 (mt0) REVERT: B 512 ARG cc_start: 0.8429 (mtp180) cc_final: 0.8044 (mmm160) REVERT: C 37 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7996 (mm) REVERT: C 44 PHE cc_start: 0.9392 (p90) cc_final: 0.8888 (p90) REVERT: C 70 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7852 (mtp) REVERT: C 98 GLU cc_start: 0.9217 (mp0) cc_final: 0.8590 (mp0) REVERT: C 136 ARG cc_start: 0.8917 (ttm110) cc_final: 0.8579 (mtp-110) REVERT: C 168 GLU cc_start: 0.8900 (mp0) cc_final: 0.8461 (pm20) REVERT: C 179 MET cc_start: 0.8676 (ptt) cc_final: 0.8287 (ptt) REVERT: C 202 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8654 (mt0) REVERT: C 206 LYS cc_start: 0.8057 (mmpt) cc_final: 0.7601 (mmmt) REVERT: C 226 ASP cc_start: 0.8961 (m-30) cc_final: 0.8727 (m-30) REVERT: C 254 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8662 (tm-30) REVERT: C 258 TYR cc_start: 0.8607 (t80) cc_final: 0.8316 (t80) REVERT: C 272 VAL cc_start: 0.8920 (t) cc_final: 0.8502 (p) REVERT: C 330 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9028 (pp) REVERT: C 352 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8715 (tm-30) REVERT: C 385 MET cc_start: 0.9231 (ttm) cc_final: 0.8915 (ttp) REVERT: C 393 THR cc_start: 0.8438 (p) cc_final: 0.7759 (t) REVERT: C 399 GLU cc_start: 0.7859 (tp30) cc_final: 0.7531 (tp30) REVERT: C 480 ARG cc_start: 0.9251 (mtm110) cc_final: 0.8981 (mtm-85) REVERT: K 1 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.2945 (pp-130) REVERT: D 37 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8096 (mm) REVERT: D 51 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8731 (pp) REVERT: D 70 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8284 (mtp) REVERT: D 98 GLU cc_start: 0.9161 (mp0) cc_final: 0.8732 (mp0) REVERT: D 136 ARG cc_start: 0.8970 (ttm110) cc_final: 0.8639 (mtp-110) REVERT: D 150 MET cc_start: 0.8453 (tmm) cc_final: 0.7882 (tmm) REVERT: D 168 GLU cc_start: 0.8982 (mp0) cc_final: 0.8560 (pm20) REVERT: D 175 LEU cc_start: 0.9471 (mp) cc_final: 0.9143 (mp) REVERT: D 179 MET cc_start: 0.8780 (ptt) cc_final: 0.8552 (ptm) REVERT: D 216 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8628 (t0) REVERT: D 254 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8591 (tm-30) REVERT: D 330 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8889 (pp) REVERT: D 352 GLU cc_start: 0.9288 (tm-30) cc_final: 0.8691 (tm-30) REVERT: D 385 MET cc_start: 0.9214 (ttm) cc_final: 0.8955 (ttp) REVERT: D 395 GLU cc_start: 0.8794 (mp0) cc_final: 0.8282 (mp0) REVERT: D 400 TYR cc_start: 0.8890 (m-10) cc_final: 0.8332 (m-10) REVERT: D 480 ARG cc_start: 0.9319 (mtm110) cc_final: 0.8884 (mtm-85) REVERT: L 1 MET cc_start: 0.5543 (OUTLIER) cc_final: 0.2456 (pp-130) REVERT: E 16 ASP cc_start: 0.8447 (t0) cc_final: 0.8154 (t0) REVERT: E 28 ASP cc_start: 0.8828 (p0) cc_final: 0.8509 (p0) REVERT: E 37 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8323 (mm) REVERT: E 51 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8832 (pp) REVERT: E 59 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8688 (pt) REVERT: E 70 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.7877 (mtp) REVERT: E 98 GLU cc_start: 0.9213 (mp0) cc_final: 0.8642 (mp0) REVERT: E 128 ARG cc_start: 0.8604 (mtp85) cc_final: 0.8206 (mtm110) REVERT: E 136 ARG cc_start: 0.8865 (ttm110) cc_final: 0.8503 (mtp-110) REVERT: E 168 GLU cc_start: 0.8960 (mp0) cc_final: 0.8547 (pm20) REVERT: E 175 LEU cc_start: 0.9350 (mp) cc_final: 0.9087 (mp) REVERT: E 226 ASP cc_start: 0.8941 (m-30) cc_final: 0.8726 (m-30) REVERT: E 254 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8696 (tm-30) REVERT: E 258 TYR cc_start: 0.8592 (t80) cc_final: 0.8111 (t80) REVERT: E 272 VAL cc_start: 0.8881 (t) cc_final: 0.8591 (p) REVERT: E 330 ILE cc_start: 0.9487 (OUTLIER) cc_final: 0.9089 (pp) REVERT: E 352 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8794 (tm-30) REVERT: E 355 ARG cc_start: 0.8993 (ptt90) cc_final: 0.8651 (ttp-170) REVERT: E 393 THR cc_start: 0.8451 (p) cc_final: 0.8128 (p) REVERT: F 37 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8133 (mm) REVERT: F 51 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8941 (pp) REVERT: F 70 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8371 (mtp) REVERT: F 78 MET cc_start: 0.9100 (tmm) cc_final: 0.8596 (tmm) REVERT: F 98 GLU cc_start: 0.9201 (mp0) cc_final: 0.8646 (mp0) REVERT: F 121 LEU cc_start: 0.8469 (mp) cc_final: 0.8268 (mt) REVERT: F 136 ARG cc_start: 0.8898 (ttm110) cc_final: 0.8579 (mtp-110) REVERT: F 164 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8215 (t70) REVERT: F 168 GLU cc_start: 0.8935 (mp0) cc_final: 0.8547 (pm20) REVERT: F 175 LEU cc_start: 0.9410 (mp) cc_final: 0.9058 (mp) REVERT: F 179 MET cc_start: 0.8713 (ptt) cc_final: 0.8491 (ptm) REVERT: F 226 ASP cc_start: 0.8951 (m-30) cc_final: 0.8696 (m-30) REVERT: F 258 TYR cc_start: 0.8507 (t80) cc_final: 0.7983 (t80) REVERT: F 330 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8913 (pp) REVERT: F 352 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8616 (tm-30) REVERT: F 385 MET cc_start: 0.9177 (ttm) cc_final: 0.8927 (ttp) REVERT: F 395 GLU cc_start: 0.8756 (mp0) cc_final: 0.8508 (mp0) REVERT: F 414 MET cc_start: 0.9164 (mmm) cc_final: 0.8961 (mmm) REVERT: F 480 ARG cc_start: 0.9294 (mtm110) cc_final: 0.9067 (mtm-85) REVERT: N 1 MET cc_start: 0.5783 (OUTLIER) cc_final: 0.2766 (pp-130) REVERT: G 16 ASP cc_start: 0.8476 (t0) cc_final: 0.8199 (t0) REVERT: G 37 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8205 (mm) REVERT: G 51 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8820 (pp) REVERT: G 70 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8285 (mtp) REVERT: G 112 GLN cc_start: 0.8750 (mm110) cc_final: 0.8376 (mm110) REVERT: G 124 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8721 (tppt) REVERT: G 136 ARG cc_start: 0.8863 (ttm110) cc_final: 0.8501 (mtp-110) REVERT: G 168 GLU cc_start: 0.8993 (mp0) cc_final: 0.8531 (pm20) REVERT: G 179 MET cc_start: 0.8727 (ptt) cc_final: 0.8473 (ptm) REVERT: G 198 ASN cc_start: 0.9416 (m-40) cc_final: 0.9205 (m-40) REVERT: G 253 HIS cc_start: 0.7652 (m-70) cc_final: 0.7419 (m-70) REVERT: G 254 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8666 (tm-30) REVERT: G 272 VAL cc_start: 0.8829 (t) cc_final: 0.8464 (p) REVERT: G 330 ILE cc_start: 0.9500 (OUTLIER) cc_final: 0.9090 (pp) REVERT: G 352 GLU cc_start: 0.9249 (tm-30) cc_final: 0.8759 (tm-30) REVERT: G 393 THR cc_start: 0.8495 (p) cc_final: 0.7836 (t) REVERT: G 480 ARG cc_start: 0.9311 (mtm110) cc_final: 0.9078 (mtm-85) REVERT: O 1 MET cc_start: 0.5689 (OUTLIER) cc_final: 0.2611 (pp-130) REVERT: H 37 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8134 (mm) REVERT: H 70 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8539 (mtp) REVERT: H 98 GLU cc_start: 0.9220 (mp0) cc_final: 0.8781 (mp0) REVERT: H 105 ARG cc_start: 0.8683 (ttp-110) cc_final: 0.8467 (ttp-110) REVERT: H 128 ARG cc_start: 0.7862 (mtm110) cc_final: 0.7575 (mtm110) REVERT: H 136 ARG cc_start: 0.8958 (ttm110) cc_final: 0.8634 (mtp-110) REVERT: H 168 GLU cc_start: 0.8997 (mp0) cc_final: 0.8582 (pm20) REVERT: H 175 LEU cc_start: 0.9456 (mp) cc_final: 0.9116 (mp) REVERT: H 179 MET cc_start: 0.8783 (ptt) cc_final: 0.8572 (ptm) REVERT: H 206 LYS cc_start: 0.8277 (mmmt) cc_final: 0.7858 (mmmt) REVERT: H 216 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8627 (t0) REVERT: H 232 ASP cc_start: 0.8888 (m-30) cc_final: 0.8571 (t0) REVERT: H 253 HIS cc_start: 0.7591 (m-70) cc_final: 0.7352 (m-70) REVERT: H 254 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8624 (tm-30) REVERT: H 265 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8471 (mm-40) REVERT: H 330 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.8885 (pp) REVERT: H 352 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8706 (tm-30) REVERT: H 385 MET cc_start: 0.9209 (ttm) cc_final: 0.8854 (ttp) REVERT: H 394 THR cc_start: 0.9298 (p) cc_final: 0.9079 (p) REVERT: H 395 GLU cc_start: 0.8614 (mp0) cc_final: 0.8395 (mp0) REVERT: H 414 MET cc_start: 0.9132 (mmm) cc_final: 0.8826 (mmm) REVERT: P 1 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.3002 (pp-130) outliers start: 233 outliers final: 146 residues processed: 1095 average time/residue: 0.1805 time to fit residues: 325.6024 Evaluate side-chains 1127 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 939 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 466 HIS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 265 GLN Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain P residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 361 optimal weight: 0.5980 chunk 195 optimal weight: 0.0970 chunk 105 optimal weight: 0.9980 chunk 243 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 345 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102829 restraints weight = 51177.671| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.48 r_work: 0.3042 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32360 Z= 0.127 Angle : 0.692 10.803 43936 Z= 0.323 Chirality : 0.047 0.172 5000 Planarity : 0.003 0.037 5456 Dihedral : 15.172 167.259 4710 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 7.09 % Allowed : 25.18 % Favored : 67.73 % 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: -1.35 (0.13), residues: 3968 helix: 0.04 (0.14), residues: 1304 sheet: -1.42 (0.23), residues: 536 loop : -1.34 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 512 TYR 0.014 0.001 TYR G 353 PHE 0.016 0.001 PHE D 165 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (32352) covalent geometry : angle 0.69235 / 0.32 (43936) hydrogen bonds : bond 0.03098 / 2.04 ( 992) hydrogen bonds : angle 4.94277 / 3.36 ( 2832) Misc. bond : bond 0.00041 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 991 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8278 (mm) REVERT: A 51 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8727 (pp) REVERT: A 70 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8337 (mtp) REVERT: A 75 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8316 (mm-30) REVERT: A 105 ARG cc_start: 0.8617 (ttp-110) cc_final: 0.8398 (ttp-110) REVERT: A 112 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7599 (mp10) REVERT: A 124 LYS cc_start: 0.9092 (mmmt) cc_final: 0.8804 (tppt) REVERT: A 136 ARG cc_start: 0.8989 (ttm110) cc_final: 0.8646 (mtp-110) REVERT: A 150 MET cc_start: 0.8480 (tmm) cc_final: 0.7919 (tmm) REVERT: A 168 GLU cc_start: 0.8998 (mp0) cc_final: 0.8579 (pm20) REVERT: A 179 MET cc_start: 0.8617 (ptt) cc_final: 0.8381 (ptm) REVERT: A 205 LYS cc_start: 0.9156 (mmtm) cc_final: 0.8949 (mptt) REVERT: A 216 ASP cc_start: 0.9113 (OUTLIER) cc_final: 0.8689 (t0) REVERT: A 272 VAL cc_start: 0.8816 (t) cc_final: 0.8485 (p) REVERT: A 330 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.8978 (pp) REVERT: A 352 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8748 (tm-30) REVERT: A 355 ARG cc_start: 0.8904 (ptt90) cc_final: 0.8637 (ttp-170) REVERT: A 385 MET cc_start: 0.9225 (ttm) cc_final: 0.8927 (ttp) REVERT: A 393 THR cc_start: 0.8476 (p) cc_final: 0.7775 (t) REVERT: A 395 GLU cc_start: 0.8788 (mp0) cc_final: 0.8459 (mp0) REVERT: A 410 LYS cc_start: 0.7930 (pttt) cc_final: 0.7603 (pttp) REVERT: I 1 MET cc_start: 0.5963 (OUTLIER) cc_final: 0.3169 (pp-130) REVERT: B 37 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7989 (mm) REVERT: B 51 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8821 (pp) REVERT: B 75 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8077 (mm-30) REVERT: B 78 MET cc_start: 0.8949 (ttp) cc_final: 0.8352 (tmm) REVERT: B 98 GLU cc_start: 0.9232 (mp0) cc_final: 0.9015 (mp0) REVERT: B 168 GLU cc_start: 0.9041 (mp0) cc_final: 0.8625 (pm20) REVERT: B 175 LEU cc_start: 0.9385 (mp) cc_final: 0.9009 (mp) REVERT: B 199 GLU cc_start: 0.9168 (pt0) cc_final: 0.8885 (pt0) REVERT: B 232 ASP cc_start: 0.8901 (m-30) cc_final: 0.8561 (t0) REVERT: B 258 TYR cc_start: 0.8611 (t80) cc_final: 0.8349 (t80) REVERT: B 272 VAL cc_start: 0.8693 (t) cc_final: 0.8338 (p) REVERT: B 330 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8880 (pp) REVERT: B 355 ARG cc_start: 0.8962 (ptt90) cc_final: 0.8712 (ttp-170) REVERT: B 385 MET cc_start: 0.9234 (ttm) cc_final: 0.8897 (ttp) REVERT: C 37 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8005 (mm) REVERT: C 44 PHE cc_start: 0.9359 (p90) cc_final: 0.8840 (p90) REVERT: C 51 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8972 (pp) REVERT: C 70 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8303 (mpp) REVERT: C 98 GLU cc_start: 0.9206 (mp0) cc_final: 0.8700 (mp0) REVERT: C 121 LEU cc_start: 0.8656 (mt) cc_final: 0.8444 (mt) REVERT: C 136 ARG cc_start: 0.8940 (ttm110) cc_final: 0.8618 (mtp-110) REVERT: C 168 GLU cc_start: 0.8943 (mp0) cc_final: 0.8574 (pm20) REVERT: C 175 LEU cc_start: 0.9549 (mp) cc_final: 0.9327 (mt) REVERT: C 179 MET cc_start: 0.8653 (ptt) cc_final: 0.8381 (ptm) REVERT: C 202 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: C 205 LYS cc_start: 0.9114 (mmtm) cc_final: 0.8816 (mptt) REVERT: C 206 LYS cc_start: 0.8032 (mmpt) cc_final: 0.7612 (mmmt) REVERT: C 226 ASP cc_start: 0.8932 (m-30) cc_final: 0.8683 (m-30) REVERT: C 254 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8570 (tm-30) REVERT: C 258 TYR cc_start: 0.8545 (t80) cc_final: 0.8271 (t80) REVERT: C 272 VAL cc_start: 0.8831 (t) cc_final: 0.8454 (p) REVERT: C 330 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9023 (pp) REVERT: C 352 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8698 (tm-30) REVERT: C 385 MET cc_start: 0.9247 (ttm) cc_final: 0.8923 (ttp) REVERT: C 393 THR cc_start: 0.8404 (p) cc_final: 0.7743 (t) REVERT: C 399 GLU cc_start: 0.7927 (tp30) cc_final: 0.7511 (tp30) REVERT: C 480 ARG cc_start: 0.9234 (mtm110) cc_final: 0.8992 (mtm-85) REVERT: K 1 MET cc_start: 0.5906 (OUTLIER) cc_final: 0.2926 (pp-130) REVERT: D 37 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8034 (mm) REVERT: D 51 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8670 (pp) REVERT: D 70 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8130 (mtp) REVERT: D 75 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7941 (mm-30) REVERT: D 136 ARG cc_start: 0.8935 (ttm110) cc_final: 0.8596 (mtp-110) REVERT: D 150 MET cc_start: 0.8435 (tmm) cc_final: 0.7895 (tmm) REVERT: D 168 GLU cc_start: 0.8996 (mp0) cc_final: 0.8574 (pm20) REVERT: D 175 LEU cc_start: 0.9468 (mp) cc_final: 0.9127 (mp) REVERT: D 179 MET cc_start: 0.8767 (ptt) cc_final: 0.8535 (ptm) REVERT: D 216 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8605 (t0) REVERT: D 254 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8591 (tm-30) REVERT: D 330 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8858 (pp) REVERT: D 385 MET cc_start: 0.9235 (ttm) cc_final: 0.8951 (ttp) REVERT: D 395 GLU cc_start: 0.8755 (mp0) cc_final: 0.8365 (mp0) REVERT: D 480 ARG cc_start: 0.9324 (mtm110) cc_final: 0.8883 (mtm-85) REVERT: L 1 MET cc_start: 0.5470 (OUTLIER) cc_final: 0.2424 (pp-130) REVERT: E 16 ASP cc_start: 0.8479 (t0) cc_final: 0.8170 (t0) REVERT: E 37 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8270 (mm) REVERT: E 51 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8803 (pp) REVERT: E 59 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8632 (pt) REVERT: E 128 ARG cc_start: 0.8645 (mtp85) cc_final: 0.8407 (mmm160) REVERT: E 136 ARG cc_start: 0.8933 (ttm110) cc_final: 0.8603 (mtp-110) REVERT: E 168 GLU cc_start: 0.8960 (mp0) cc_final: 0.8624 (pm20) REVERT: E 175 LEU cc_start: 0.9274 (mp) cc_final: 0.9018 (mp) REVERT: E 216 ASP cc_start: 0.9036 (OUTLIER) cc_final: 0.8619 (t0) REVERT: E 258 TYR cc_start: 0.8550 (t80) cc_final: 0.8185 (t80) REVERT: E 272 VAL cc_start: 0.8886 (t) cc_final: 0.8596 (p) REVERT: E 330 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.9091 (pp) REVERT: E 352 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8736 (tm-30) REVERT: E 383 THR cc_start: 0.9401 (p) cc_final: 0.9107 (t) REVERT: E 385 MET cc_start: 0.9229 (ttm) cc_final: 0.8795 (ttp) REVERT: E 393 THR cc_start: 0.8378 (p) cc_final: 0.8124 (p) REVERT: F 37 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8161 (mm) REVERT: F 51 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8841 (pp) REVERT: F 70 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8405 (mtp) REVERT: F 75 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8085 (mm-30) REVERT: F 78 MET cc_start: 0.9101 (tmm) cc_final: 0.8403 (tmm) REVERT: F 82 MET cc_start: 0.9467 (mmm) cc_final: 0.9158 (tpp) REVERT: F 98 GLU cc_start: 0.9183 (mp0) cc_final: 0.8832 (mp0) REVERT: F 136 ARG cc_start: 0.8886 (ttm110) cc_final: 0.8563 (mtp-110) REVERT: F 150 MET cc_start: 0.8488 (tmm) cc_final: 0.7927 (tmm) REVERT: F 168 GLU cc_start: 0.8951 (mp0) cc_final: 0.8562 (pm20) REVERT: F 175 LEU cc_start: 0.9413 (mp) cc_final: 0.9051 (mp) REVERT: F 179 MET cc_start: 0.8662 (ptt) cc_final: 0.8419 (ptm) REVERT: F 199 GLU cc_start: 0.9205 (pt0) cc_final: 0.8925 (pt0) REVERT: F 226 ASP cc_start: 0.8932 (m-30) cc_final: 0.8668 (m-30) REVERT: F 254 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8571 (tm-30) REVERT: F 330 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8881 (pp) REVERT: F 385 MET cc_start: 0.9185 (ttm) cc_final: 0.8872 (ttp) REVERT: F 395 GLU cc_start: 0.8756 (mp0) cc_final: 0.8522 (mp0) REVERT: F 480 ARG cc_start: 0.9313 (mtm110) cc_final: 0.9105 (mtm-85) REVERT: N 1 MET cc_start: 0.5768 (OUTLIER) cc_final: 0.2744 (pp-130) REVERT: G 16 ASP cc_start: 0.8516 (t0) cc_final: 0.8254 (t0) REVERT: G 37 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8146 (mm) REVERT: G 51 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8785 (pp) REVERT: G 70 MET cc_start: 0.8942 (mpp) cc_final: 0.7990 (mtp) REVERT: G 112 GLN cc_start: 0.8817 (mm110) cc_final: 0.8151 (mm110) REVERT: G 124 LYS cc_start: 0.9007 (mmmt) cc_final: 0.8801 (tppt) REVERT: G 136 ARG cc_start: 0.8910 (ttm110) cc_final: 0.8586 (mtp-110) REVERT: G 150 MET cc_start: 0.8461 (tmm) cc_final: 0.7847 (tmm) REVERT: G 168 GLU cc_start: 0.9031 (mp0) cc_final: 0.8616 (pm20) REVERT: G 205 LYS cc_start: 0.9259 (mptt) cc_final: 0.8921 (mmtm) REVERT: G 216 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8583 (t0) REVERT: G 224 ARG cc_start: 0.8658 (ttt90) cc_final: 0.8338 (ttt90) REVERT: G 254 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8636 (tm-30) REVERT: G 258 TYR cc_start: 0.8778 (t80) cc_final: 0.8298 (t80) REVERT: G 272 VAL cc_start: 0.8773 (t) cc_final: 0.8426 (p) REVERT: G 330 ILE cc_start: 0.9483 (OUTLIER) cc_final: 0.9085 (pp) REVERT: G 352 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8736 (tm-30) REVERT: G 393 THR cc_start: 0.8415 (p) cc_final: 0.7785 (t) REVERT: O 1 MET cc_start: 0.5634 (OUTLIER) cc_final: 0.2540 (pp-130) REVERT: H 37 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.8029 (mm) REVERT: H 70 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8521 (mtp) REVERT: H 75 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8115 (mm-30) REVERT: H 112 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8133 (mp10) REVERT: H 136 ARG cc_start: 0.8949 (ttm110) cc_final: 0.8613 (mtp-110) REVERT: H 150 MET cc_start: 0.8459 (tmm) cc_final: 0.7908 (tmm) REVERT: H 168 GLU cc_start: 0.9021 (mp0) cc_final: 0.8672 (pm20) REVERT: H 175 LEU cc_start: 0.9464 (mp) cc_final: 0.9105 (mp) REVERT: H 206 LYS cc_start: 0.8308 (mmmt) cc_final: 0.7878 (mmmt) REVERT: H 216 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8603 (t0) REVERT: H 232 ASP cc_start: 0.8873 (m-30) cc_final: 0.8522 (t0) REVERT: H 330 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8854 (pp) REVERT: H 352 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8677 (tm-30) REVERT: H 385 MET cc_start: 0.9161 (ttm) cc_final: 0.8725 (ttp) REVERT: H 393 THR cc_start: 0.8332 (p) cc_final: 0.7623 (t) REVERT: H 395 GLU cc_start: 0.8495 (mp0) cc_final: 0.8223 (mp0) REVERT: P 1 MET cc_start: 0.5984 (OUTLIER) cc_final: 0.2980 (pp-130) outliers start: 232 outliers final: 140 residues processed: 1088 average time/residue: 0.1855 time to fit residues: 331.4299 Evaluate side-chains 1126 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 945 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 466 HIS Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 309 GLN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain P residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 275 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 302 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 299 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 379 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 HIS A 94 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS E 94 ASN ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.098504 restraints weight = 51659.486| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.45 r_work: 0.2982 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32360 Z= 0.175 Angle : 0.718 10.739 43936 Z= 0.341 Chirality : 0.049 0.168 5000 Planarity : 0.004 0.045 5456 Dihedral : 15.184 167.977 4710 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 7.55 % Allowed : 25.61 % Favored : 66.84 % 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: -1.29 (0.13), residues: 3968 helix: 0.00 (0.14), residues: 1304 sheet: -1.41 (0.22), residues: 552 loop : -1.22 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 105 TYR 0.020 0.001 TYR A 258 PHE 0.014 0.001 PHE B 165 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (32352) covalent geometry : angle 0.71782 / 0.34 (43936) hydrogen bonds : bond 0.03182 / 2.09 ( 992) hydrogen bonds : angle 4.99038 / 3.40 ( 2832) Misc. bond : bond 0.00092 / 0.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 247 poor density : 946 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8248 (mm) REVERT: A 51 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8816 (pp) REVERT: A 70 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8388 (mtp) REVERT: A 75 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8206 (mm-30) REVERT: A 124 LYS cc_start: 0.9071 (mmmt) cc_final: 0.8794 (tppt) REVERT: A 136 ARG cc_start: 0.9036 (ttm110) cc_final: 0.8692 (mtp-110) REVERT: A 168 GLU cc_start: 0.8986 (mp0) cc_final: 0.8578 (pm20) REVERT: A 179 MET cc_start: 0.8768 (ptt) cc_final: 0.8500 (ptm) REVERT: A 216 ASP cc_start: 0.9084 (OUTLIER) cc_final: 0.8711 (t0) REVERT: A 272 VAL cc_start: 0.8838 (t) cc_final: 0.8515 (p) REVERT: A 274 ASP cc_start: 0.8957 (t0) cc_final: 0.8686 (t0) REVERT: A 330 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9002 (pp) REVERT: A 352 GLU cc_start: 0.9255 (tm-30) cc_final: 0.8825 (tm-30) REVERT: A 355 ARG cc_start: 0.8971 (ptt90) cc_final: 0.8642 (ttp-170) REVERT: A 385 MET cc_start: 0.9225 (ttm) cc_final: 0.8960 (ttp) REVERT: I 1 MET cc_start: 0.5882 (OUTLIER) cc_final: 0.2935 (pp-130) REVERT: B 37 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8033 (mm) REVERT: B 51 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8854 (pp) REVERT: B 75 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7974 (mm-30) REVERT: B 78 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8152 (tmm) REVERT: B 128 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6240 (mtm-85) REVERT: B 168 GLU cc_start: 0.9053 (mp0) cc_final: 0.8675 (pm20) REVERT: B 175 LEU cc_start: 0.9453 (mp) cc_final: 0.9208 (mp) REVERT: B 199 GLU cc_start: 0.9185 (pt0) cc_final: 0.8821 (pt0) REVERT: B 254 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8586 (tm-30) REVERT: B 258 TYR cc_start: 0.8591 (t80) cc_final: 0.8105 (t80) REVERT: B 272 VAL cc_start: 0.8729 (t) cc_final: 0.8391 (p) REVERT: B 330 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.8913 (pp) REVERT: B 385 MET cc_start: 0.9248 (ttm) cc_final: 0.8966 (ttp) REVERT: C 37 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8169 (mm) REVERT: C 51 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9015 (pp) REVERT: C 70 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.7333 (mpp) REVERT: C 75 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8085 (mm-30) REVERT: C 98 GLU cc_start: 0.9250 (mp0) cc_final: 0.8754 (mp0) REVERT: C 136 ARG cc_start: 0.8978 (ttm110) cc_final: 0.8647 (mtp-110) REVERT: C 168 GLU cc_start: 0.8942 (mp0) cc_final: 0.8622 (pm20) REVERT: C 175 LEU cc_start: 0.9425 (mp) cc_final: 0.9203 (mt) REVERT: C 179 MET cc_start: 0.8722 (ptt) cc_final: 0.8445 (ptm) REVERT: C 202 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8635 (tt0) REVERT: C 216 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8612 (t0) REVERT: C 254 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8504 (tm-30) REVERT: C 258 TYR cc_start: 0.8633 (t80) cc_final: 0.8353 (t80) REVERT: C 272 VAL cc_start: 0.8889 (t) cc_final: 0.8549 (p) REVERT: C 330 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9064 (pp) REVERT: C 352 GLU cc_start: 0.9254 (tm-30) cc_final: 0.8759 (tm-30) REVERT: C 385 MET cc_start: 0.9263 (ttm) cc_final: 0.8905 (ttp) REVERT: K 1 MET cc_start: 0.6116 (OUTLIER) cc_final: 0.3069 (pp-130) REVERT: D 37 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7973 (mm) REVERT: D 51 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8758 (pp) REVERT: D 70 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8153 (mtp) REVERT: D 78 MET cc_start: 0.8903 (ttp) cc_final: 0.8670 (ttp) REVERT: D 112 GLN cc_start: 0.8728 (mm110) cc_final: 0.8427 (mm-40) REVERT: D 136 ARG cc_start: 0.8974 (ttm110) cc_final: 0.8649 (mtp-110) REVERT: D 168 GLU cc_start: 0.8993 (mp0) cc_final: 0.8575 (pm20) REVERT: D 175 LEU cc_start: 0.9489 (mp) cc_final: 0.9140 (mp) REVERT: D 179 MET cc_start: 0.8774 (ptt) cc_final: 0.8526 (ptm) REVERT: D 216 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8593 (t0) REVERT: D 254 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8578 (tm-30) REVERT: D 330 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.8913 (pp) REVERT: D 385 MET cc_start: 0.9226 (ttm) cc_final: 0.8910 (ttp) REVERT: D 395 GLU cc_start: 0.8796 (mp0) cc_final: 0.8483 (mp0) REVERT: D 480 ARG cc_start: 0.9317 (mtm110) cc_final: 0.8920 (mtm-85) REVERT: L 1 MET cc_start: 0.5677 (OUTLIER) cc_final: 0.2661 (pp-130) REVERT: E 16 ASP cc_start: 0.8420 (t0) cc_final: 0.8146 (t0) REVERT: E 37 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8319 (mm) REVERT: E 51 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8897 (pp) REVERT: E 59 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8707 (pt) REVERT: E 70 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8253 (mtp) REVERT: E 128 ARG cc_start: 0.8631 (mtp85) cc_final: 0.8374 (mmm160) REVERT: E 136 ARG cc_start: 0.8931 (ttm110) cc_final: 0.8600 (mtp-110) REVERT: E 168 GLU cc_start: 0.9023 (mp0) cc_final: 0.8709 (pm20) REVERT: E 175 LEU cc_start: 0.9297 (mp) cc_final: 0.9088 (mp) REVERT: E 216 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8611 (t0) REVERT: E 254 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8621 (tm-30) REVERT: E 258 TYR cc_start: 0.8546 (t80) cc_final: 0.8221 (t80) REVERT: E 265 GLN cc_start: 0.8827 (mp10) cc_final: 0.8587 (mt0) REVERT: E 272 VAL cc_start: 0.8902 (t) cc_final: 0.8630 (p) REVERT: E 330 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9112 (pp) REVERT: E 352 GLU cc_start: 0.9301 (tm-30) cc_final: 0.8822 (tm-30) REVERT: E 393 THR cc_start: 0.8534 (p) cc_final: 0.8268 (p) REVERT: F 37 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8259 (mm) REVERT: F 70 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8306 (mtp) REVERT: F 75 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7982 (mm-30) REVERT: F 78 MET cc_start: 0.9117 (tmm) cc_final: 0.8209 (tmm) REVERT: F 136 ARG cc_start: 0.8898 (ttm110) cc_final: 0.8588 (mtp-110) REVERT: F 168 GLU cc_start: 0.8966 (mp0) cc_final: 0.8652 (pm20) REVERT: F 175 LEU cc_start: 0.9443 (mp) cc_final: 0.9077 (mp) REVERT: F 179 MET cc_start: 0.8744 (ptt) cc_final: 0.8452 (ptm) REVERT: F 258 TYR cc_start: 0.8560 (t80) cc_final: 0.8210 (t80) REVERT: F 330 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.8929 (pp) REVERT: F 385 MET cc_start: 0.9228 (ttm) cc_final: 0.8923 (ttp) REVERT: F 395 GLU cc_start: 0.8723 (mp0) cc_final: 0.8444 (mp0) REVERT: F 480 ARG cc_start: 0.9312 (mtm110) cc_final: 0.9069 (mtm-85) REVERT: F 505 SER cc_start: 0.9061 (t) cc_final: 0.8613 (p) REVERT: N 1 MET cc_start: 0.5708 (OUTLIER) cc_final: 0.2696 (pp-130) REVERT: G 37 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8152 (mm) REVERT: G 51 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8820 (pp) REVERT: G 59 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8779 (pt) REVERT: G 70 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8367 (mtp) REVERT: G 112 GLN cc_start: 0.8803 (mm110) cc_final: 0.8014 (mm110) REVERT: G 136 ARG cc_start: 0.8897 (ttm110) cc_final: 0.8567 (mtp-110) REVERT: G 150 MET cc_start: 0.8404 (tmm) cc_final: 0.7805 (tmm) REVERT: G 168 GLU cc_start: 0.9061 (mp0) cc_final: 0.8685 (pm20) REVERT: G 216 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8575 (t0) REVERT: G 254 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8593 (tm-30) REVERT: G 258 TYR cc_start: 0.8836 (t80) cc_final: 0.8334 (t80) REVERT: G 272 VAL cc_start: 0.8815 (t) cc_final: 0.8490 (p) REVERT: G 330 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9096 (pp) REVERT: G 352 GLU cc_start: 0.9260 (tm-30) cc_final: 0.8774 (tm-30) REVERT: G 393 THR cc_start: 0.8630 (p) cc_final: 0.8398 (p) REVERT: O 1 MET cc_start: 0.5712 (OUTLIER) cc_final: 0.2673 (pp-130) REVERT: H 37 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8111 (mm) REVERT: H 70 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8284 (mtp) REVERT: H 75 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8013 (mm-30) REVERT: H 112 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8291 (mm-40) REVERT: H 128 ARG cc_start: 0.8950 (mmm-85) cc_final: 0.8737 (mmm-85) REVERT: H 136 ARG cc_start: 0.8950 (ttm110) cc_final: 0.8664 (mtp-110) REVERT: H 150 MET cc_start: 0.8399 (tmm) cc_final: 0.7847 (tmm) REVERT: H 166 LEU cc_start: 0.8723 (mp) cc_final: 0.8179 (mm) REVERT: H 168 GLU cc_start: 0.9049 (mp0) cc_final: 0.8648 (pm20) REVERT: H 175 LEU cc_start: 0.9502 (mp) cc_final: 0.9263 (mp) REVERT: H 206 LYS cc_start: 0.8408 (mmmt) cc_final: 0.7999 (mmmt) REVERT: H 253 HIS cc_start: 0.7770 (m-70) cc_final: 0.7540 (m-70) REVERT: H 254 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8632 (tm-30) REVERT: H 330 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8891 (pp) REVERT: H 352 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8733 (tm-30) REVERT: H 393 THR cc_start: 0.8579 (p) cc_final: 0.8231 (p) REVERT: H 395 GLU cc_start: 0.8699 (mp0) cc_final: 0.8482 (mp0) REVERT: P 1 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.3069 (pp-130) outliers start: 247 outliers final: 173 residues processed: 1049 average time/residue: 0.1780 time to fit residues: 309.8711 Evaluate side-chains 1137 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 918 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 466 HIS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 309 GLN Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain P residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 222 optimal weight: 2.9990 chunk 335 optimal weight: 7.9990 chunk 327 optimal weight: 0.9980 chunk 378 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 313 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 375 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 HIS ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.132749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.098320 restraints weight = 51737.701| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.42 r_work: 0.2972 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32360 Z= 0.178 Angle : 0.730 10.991 43936 Z= 0.347 Chirality : 0.049 0.204 5000 Planarity : 0.004 0.057 5456 Dihedral : 15.170 167.871 4710 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 7.52 % Allowed : 25.83 % Favored : 66.66 % 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: -1.26 (0.13), residues: 3968 helix: -0.02 (0.14), residues: 1304 sheet: -1.54 (0.22), residues: 536 loop : -1.12 (0.14), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 105 TYR 0.014 0.001 TYR E 353 PHE 0.014 0.001 PHE H 401 HIS 0.005 0.001 HIS F 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (32352) covalent geometry : angle 0.72974 / 0.35 (43936) hydrogen bonds : bond 0.03195 / 2.11 ( 992) hydrogen bonds : angle 5.05061 / 3.43 ( 2832) Misc. bond : bond 0.00100 / 0.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 920 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8202 (mm) REVERT: A 51 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8830 (pp) REVERT: A 70 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.7648 (mpp) REVERT: A 75 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7992 (mm-30) REVERT: A 124 LYS cc_start: 0.9092 (mmmt) cc_final: 0.8799 (tppt) REVERT: A 136 ARG cc_start: 0.9028 (ttm110) cc_final: 0.8685 (mtp-110) REVERT: A 150 MET cc_start: 0.8442 (tmm) cc_final: 0.7878 (tmm) REVERT: A 168 GLU cc_start: 0.9002 (mp0) cc_final: 0.8532 (pm20) REVERT: A 179 MET cc_start: 0.8707 (ptt) cc_final: 0.8465 (ptm) REVERT: A 205 LYS cc_start: 0.9135 (mmtm) cc_final: 0.8932 (mptt) REVERT: A 216 ASP cc_start: 0.9072 (OUTLIER) cc_final: 0.8694 (t0) REVERT: A 272 VAL cc_start: 0.8827 (t) cc_final: 0.8552 (p) REVERT: A 274 ASP cc_start: 0.8988 (t0) cc_final: 0.8702 (t0) REVERT: A 330 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9020 (pp) REVERT: A 352 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8764 (tm-30) REVERT: A 385 MET cc_start: 0.9208 (ttm) cc_final: 0.8955 (ttp) REVERT: I 1 MET cc_start: 0.6087 (OUTLIER) cc_final: 0.3078 (pp-130) REVERT: B 37 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8019 (mm) REVERT: B 51 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8844 (pp) REVERT: B 75 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7982 (mm-30) REVERT: B 78 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8086 (tmm) REVERT: B 112 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8086 (mp10) REVERT: B 128 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6992 (mpp-170) REVERT: B 168 GLU cc_start: 0.9046 (mp0) cc_final: 0.8767 (pm20) REVERT: B 175 LEU cc_start: 0.9369 (mp) cc_final: 0.9152 (mp) REVERT: B 199 GLU cc_start: 0.9184 (pt0) cc_final: 0.8811 (pt0) REVERT: B 216 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8580 (t0) REVERT: B 232 ASP cc_start: 0.8845 (m-30) cc_final: 0.8473 (t0) REVERT: B 254 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8542 (tm-30) REVERT: B 258 TYR cc_start: 0.8496 (t80) cc_final: 0.8048 (t80) REVERT: B 272 VAL cc_start: 0.8715 (t) cc_final: 0.8390 (p) REVERT: B 330 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.8934 (pp) REVERT: B 385 MET cc_start: 0.9249 (ttm) cc_final: 0.8988 (ttp) REVERT: C 37 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8122 (mm) REVERT: C 51 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8982 (pp) REVERT: C 70 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8243 (mtp) REVERT: C 75 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8004 (mm-30) REVERT: C 98 GLU cc_start: 0.9219 (mp0) cc_final: 0.8732 (mp0) REVERT: C 112 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8042 (mp10) REVERT: C 136 ARG cc_start: 0.8957 (ttm110) cc_final: 0.8630 (mtp-110) REVERT: C 168 GLU cc_start: 0.8967 (mp0) cc_final: 0.8631 (pm20) REVERT: C 175 LEU cc_start: 0.9443 (mp) cc_final: 0.9161 (mp) REVERT: C 179 MET cc_start: 0.8671 (ptt) cc_final: 0.8443 (ptm) REVERT: C 202 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8773 (tt0) REVERT: C 216 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8603 (t0) REVERT: C 254 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8442 (tm-30) REVERT: C 258 TYR cc_start: 0.8647 (t80) cc_final: 0.8372 (t80) REVERT: C 272 VAL cc_start: 0.8869 (t) cc_final: 0.8567 (p) REVERT: C 330 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9042 (pp) REVERT: C 385 MET cc_start: 0.9274 (ttm) cc_final: 0.8932 (ttp) REVERT: K 1 MET cc_start: 0.5935 (OUTLIER) cc_final: 0.2810 (pp-130) REVERT: D 37 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7987 (mm) REVERT: D 51 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8778 (pp) REVERT: D 70 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8241 (mtp) REVERT: D 112 GLN cc_start: 0.8718 (mm110) cc_final: 0.7375 (mp10) REVERT: D 136 ARG cc_start: 0.8978 (ttm110) cc_final: 0.8644 (mtp-110) REVERT: D 150 MET cc_start: 0.8382 (tmm) cc_final: 0.7849 (tmm) REVERT: D 168 GLU cc_start: 0.9040 (mp0) cc_final: 0.8606 (pm20) REVERT: D 175 LEU cc_start: 0.9504 (mp) cc_final: 0.9158 (mp) REVERT: D 179 MET cc_start: 0.8759 (ptt) cc_final: 0.8554 (ptm) REVERT: D 198 ASN cc_start: 0.9431 (m-40) cc_final: 0.9132 (m-40) REVERT: D 216 ASP cc_start: 0.8997 (OUTLIER) cc_final: 0.8602 (t0) REVERT: D 254 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8487 (tm-30) REVERT: D 330 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.8926 (pp) REVERT: D 385 MET cc_start: 0.9232 (ttm) cc_final: 0.8880 (ttp) REVERT: D 395 GLU cc_start: 0.8750 (mp0) cc_final: 0.8499 (mp0) REVERT: L 1 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.2809 (pp-130) REVERT: E 16 ASP cc_start: 0.8369 (t0) cc_final: 0.8093 (t0) REVERT: E 37 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8220 (mm) REVERT: E 51 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8944 (pp) REVERT: E 70 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8339 (mtp) REVERT: E 136 ARG cc_start: 0.8925 (ttm110) cc_final: 0.8598 (mtp-110) REVERT: E 168 GLU cc_start: 0.9027 (mp0) cc_final: 0.8705 (pm20) REVERT: E 175 LEU cc_start: 0.9327 (mp) cc_final: 0.9045 (mp) REVERT: E 254 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8602 (tm-30) REVERT: E 258 TYR cc_start: 0.8528 (t80) cc_final: 0.8212 (t80) REVERT: E 265 GLN cc_start: 0.8867 (mp10) cc_final: 0.8619 (mt0) REVERT: E 272 VAL cc_start: 0.8884 (t) cc_final: 0.8618 (p) REVERT: E 325 MET cc_start: 0.8552 (ttm) cc_final: 0.8201 (ttt) REVERT: E 330 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9100 (pp) REVERT: E 352 GLU cc_start: 0.9312 (tm-30) cc_final: 0.8822 (tm-30) REVERT: E 383 THR cc_start: 0.9404 (p) cc_final: 0.9123 (t) REVERT: F 37 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8112 (mm) REVERT: F 70 MET cc_start: 0.8944 (mpp) cc_final: 0.8490 (mtp) REVERT: F 75 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8010 (mm-30) REVERT: F 94 ASN cc_start: 0.8984 (t0) cc_final: 0.8771 (t0) REVERT: F 136 ARG cc_start: 0.8908 (ttm110) cc_final: 0.8541 (mtp-110) REVERT: F 168 GLU cc_start: 0.9074 (mp0) cc_final: 0.8639 (pm20) REVERT: F 175 LEU cc_start: 0.9447 (mp) cc_final: 0.9074 (mp) REVERT: F 179 MET cc_start: 0.8667 (ptt) cc_final: 0.8433 (ptm) REVERT: F 199 GLU cc_start: 0.9194 (pt0) cc_final: 0.8864 (pt0) REVERT: F 254 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8551 (tm-30) REVERT: F 258 TYR cc_start: 0.8511 (t80) cc_final: 0.8179 (t80) REVERT: F 330 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.8917 (pp) REVERT: F 385 MET cc_start: 0.9234 (ttm) cc_final: 0.8936 (ttp) REVERT: F 480 ARG cc_start: 0.9316 (mtm110) cc_final: 0.9062 (mtm-85) REVERT: F 505 SER cc_start: 0.9065 (t) cc_final: 0.8627 (p) REVERT: N 1 MET cc_start: 0.5878 (OUTLIER) cc_final: 0.2803 (pp-130) REVERT: G 37 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8132 (mm) REVERT: G 51 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8839 (pp) REVERT: G 59 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8798 (pt) REVERT: G 70 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8338 (mtp) REVERT: G 136 ARG cc_start: 0.8902 (ttm110) cc_final: 0.8569 (mtp-110) REVERT: G 150 MET cc_start: 0.8481 (tmm) cc_final: 0.7958 (tmm) REVERT: G 168 GLU cc_start: 0.9050 (mp0) cc_final: 0.8646 (pm20) REVERT: G 216 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8609 (t0) REVERT: G 254 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8541 (tm-30) REVERT: G 258 TYR cc_start: 0.8791 (t80) cc_final: 0.8378 (t80) REVERT: G 272 VAL cc_start: 0.8809 (t) cc_final: 0.8481 (p) REVERT: G 330 ILE cc_start: 0.9479 (OUTLIER) cc_final: 0.9061 (pp) REVERT: G 352 GLU cc_start: 0.9270 (tm-30) cc_final: 0.8778 (tm-30) REVERT: G 393 THR cc_start: 0.8663 (p) cc_final: 0.8419 (p) REVERT: O 1 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.4931 (pmm) REVERT: H 37 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.8028 (mm) REVERT: H 70 MET cc_start: 0.8959 (mpp) cc_final: 0.8557 (mtp) REVERT: H 75 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7995 (mm-30) REVERT: H 128 ARG cc_start: 0.8961 (mmm-85) cc_final: 0.8714 (mmm-85) REVERT: H 136 ARG cc_start: 0.8943 (ttm110) cc_final: 0.8581 (mtp-110) REVERT: H 150 MET cc_start: 0.8446 (tmm) cc_final: 0.7885 (tmm) REVERT: H 168 GLU cc_start: 0.9093 (mp0) cc_final: 0.8774 (pm20) REVERT: H 175 LEU cc_start: 0.9470 (mp) cc_final: 0.9171 (mp) REVERT: H 206 LYS cc_start: 0.8446 (mmmt) cc_final: 0.8008 (mmmt) REVERT: H 216 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8658 (t0) REVERT: H 330 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.8894 (pp) REVERT: H 352 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8713 (tm-30) REVERT: H 393 THR cc_start: 0.8677 (p) cc_final: 0.8369 (p) REVERT: H 395 GLU cc_start: 0.8697 (mp0) cc_final: 0.8439 (mp0) REVERT: P 1 MET cc_start: 0.6051 (OUTLIER) cc_final: 0.2989 (pp-130) outliers start: 246 outliers final: 183 residues processed: 1012 average time/residue: 0.1708 time to fit residues: 286.6157 Evaluate side-chains 1118 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 891 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 466 HIS Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 309 GLN Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 510 GLU Chi-restraints excluded: chain P residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 4 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 333 optimal weight: 0.9980 chunk 258 optimal weight: 0.0870 chunk 322 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 HIS ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.135230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100571 restraints weight = 51264.315| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.47 r_work: 0.3016 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32360 Z= 0.133 Angle : 0.714 11.646 43936 Z= 0.336 Chirality : 0.048 0.166 5000 Planarity : 0.003 0.034 5456 Dihedral : 14.971 167.803 4710 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 6.75 % Allowed : 26.89 % Favored : 66.35 % 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: -1.19 (0.13), residues: 3968 helix: 0.06 (0.14), residues: 1296 sheet: -1.53 (0.22), residues: 536 loop : -1.09 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 105 TYR 0.022 0.001 TYR A 258 PHE 0.013 0.001 PHE B 165 HIS 0.006 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (32352) covalent geometry : angle 0.71425 / 0.34 (43936) hydrogen bonds : bond 0.03114 / 2.06 ( 992) hydrogen bonds : angle 4.98359 / 3.39 ( 2832) Misc. bond : bond 0.00041 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 944 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8096 (mm) REVERT: A 51 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8737 (pp) REVERT: A 70 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.7306 (mpp) REVERT: A 75 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8097 (mm-30) REVERT: A 124 LYS cc_start: 0.9091 (mmmt) cc_final: 0.8776 (tppt) REVERT: A 128 ARG cc_start: 0.8593 (mtp-110) cc_final: 0.8322 (mtm110) REVERT: A 136 ARG cc_start: 0.9020 (ttm110) cc_final: 0.8682 (mtp-110) REVERT: A 150 MET cc_start: 0.8427 (tmm) cc_final: 0.7849 (tmm) REVERT: A 168 GLU cc_start: 0.9026 (mp0) cc_final: 0.8513 (pm20) REVERT: A 216 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8688 (t0) REVERT: A 224 ARG cc_start: 0.8670 (ttt90) cc_final: 0.8255 (ttt90) REVERT: A 272 VAL cc_start: 0.8779 (t) cc_final: 0.8501 (p) REVERT: A 330 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9020 (pp) REVERT: A 352 GLU cc_start: 0.9258 (tm-30) cc_final: 0.8747 (tm-30) REVERT: A 385 MET cc_start: 0.9175 (ttm) cc_final: 0.8914 (ttp) REVERT: A 393 THR cc_start: 0.8571 (p) cc_final: 0.8326 (p) REVERT: A 469 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8991 (tt0) REVERT: I 1 MET cc_start: 0.6053 (OUTLIER) cc_final: 0.3097 (pp-130) REVERT: B 37 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7897 (mm) REVERT: B 51 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8827 (pp) REVERT: B 75 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7988 (mm-30) REVERT: B 112 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8154 (mp10) REVERT: B 128 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7183 (mpp-170) REVERT: B 168 GLU cc_start: 0.9056 (mp0) cc_final: 0.8720 (pm20) REVERT: B 199 GLU cc_start: 0.9165 (pt0) cc_final: 0.8786 (pt0) REVERT: B 216 ASP cc_start: 0.8981 (OUTLIER) cc_final: 0.8547 (t0) REVERT: B 232 ASP cc_start: 0.8862 (m-30) cc_final: 0.8418 (t0) REVERT: B 258 TYR cc_start: 0.8514 (t80) cc_final: 0.8063 (t80) REVERT: B 272 VAL cc_start: 0.8701 (t) cc_final: 0.8373 (p) REVERT: B 330 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.8935 (pp) REVERT: B 385 MET cc_start: 0.9242 (ttm) cc_final: 0.8996 (ttp) REVERT: B 469 GLN cc_start: 0.9273 (tm-30) cc_final: 0.9012 (tt0) REVERT: C 37 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8080 (mm) REVERT: C 51 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8916 (pp) REVERT: C 70 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7170 (mpp) REVERT: C 75 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8049 (mm-30) REVERT: C 136 ARG cc_start: 0.8904 (ttm110) cc_final: 0.8549 (mtp-110) REVERT: C 168 GLU cc_start: 0.8951 (mp0) cc_final: 0.8630 (pm20) REVERT: C 175 LEU cc_start: 0.9411 (mp) cc_final: 0.9124 (mp) REVERT: C 179 MET cc_start: 0.8701 (ptt) cc_final: 0.8476 (ptm) REVERT: C 202 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8671 (mt0) REVERT: C 216 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8527 (t0) REVERT: C 254 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8430 (tm-30) REVERT: C 272 VAL cc_start: 0.8824 (t) cc_final: 0.8508 (p) REVERT: C 330 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9020 (pp) REVERT: C 337 LEU cc_start: 0.8507 (mp) cc_final: 0.8273 (mp) REVERT: C 385 MET cc_start: 0.9259 (ttm) cc_final: 0.8914 (ttp) REVERT: C 469 GLN cc_start: 0.9275 (tm-30) cc_final: 0.8981 (tt0) REVERT: C 480 ARG cc_start: 0.9244 (mtm110) cc_final: 0.8994 (mtm-85) REVERT: C 512 ARG cc_start: 0.8395 (mtp180) cc_final: 0.8060 (mmm160) REVERT: K 1 MET cc_start: 0.6262 (OUTLIER) cc_final: 0.3272 (pp-130) REVERT: D 37 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7930 (mm) REVERT: D 51 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8646 (pp) REVERT: D 70 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.7638 (mpp) REVERT: D 78 MET cc_start: 0.8863 (ttp) cc_final: 0.8646 (ttp) REVERT: D 112 GLN cc_start: 0.8746 (mm110) cc_final: 0.7410 (mp10) REVERT: D 136 ARG cc_start: 0.8936 (ttm110) cc_final: 0.8577 (mtp-110) REVERT: D 150 MET cc_start: 0.8299 (tmm) cc_final: 0.7719 (tmm) REVERT: D 168 GLU cc_start: 0.9046 (mp0) cc_final: 0.8609 (pm20) REVERT: D 175 LEU cc_start: 0.9497 (mp) cc_final: 0.9141 (mp) REVERT: D 216 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8598 (t0) REVERT: D 254 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8489 (tm-30) REVERT: D 330 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.8942 (pp) REVERT: D 385 MET cc_start: 0.9199 (ttm) cc_final: 0.8837 (ttp) REVERT: D 395 GLU cc_start: 0.8835 (mp0) cc_final: 0.8544 (mp0) REVERT: D 469 GLN cc_start: 0.9350 (tm-30) cc_final: 0.8604 (tt0) REVERT: D 480 ARG cc_start: 0.9314 (mtm110) cc_final: 0.9058 (mtm-85) REVERT: L 1 MET cc_start: 0.5742 (OUTLIER) cc_final: 0.2734 (pp-130) REVERT: E 16 ASP cc_start: 0.8390 (t0) cc_final: 0.8068 (t0) REVERT: E 37 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8109 (mm) REVERT: E 51 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8798 (pp) REVERT: E 70 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.7405 (mpp) REVERT: E 112 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8246 (mp10) REVERT: E 136 ARG cc_start: 0.8909 (ttm110) cc_final: 0.8552 (mtp-110) REVERT: E 168 GLU cc_start: 0.9070 (mp0) cc_final: 0.8641 (pm20) REVERT: E 175 LEU cc_start: 0.9326 (mp) cc_final: 0.9098 (mp) REVERT: E 224 ARG cc_start: 0.8692 (ttt90) cc_final: 0.8309 (ttt90) REVERT: E 254 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8542 (tm-30) REVERT: E 258 TYR cc_start: 0.8500 (t80) cc_final: 0.8292 (t80) REVERT: E 265 GLN cc_start: 0.8797 (mp10) cc_final: 0.8571 (mt0) REVERT: E 272 VAL cc_start: 0.8871 (t) cc_final: 0.8608 (p) REVERT: E 330 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9140 (pp) REVERT: E 352 GLU cc_start: 0.9271 (tm-30) cc_final: 0.8810 (tm-30) REVERT: E 383 THR cc_start: 0.9344 (p) cc_final: 0.9076 (t) REVERT: E 469 GLN cc_start: 0.9203 (tm-30) cc_final: 0.8932 (tt0) REVERT: F 37 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8095 (mm) REVERT: F 70 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8435 (mtp) REVERT: F 75 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7977 (mm-30) REVERT: F 136 ARG cc_start: 0.8886 (ttm110) cc_final: 0.8532 (mtp-110) REVERT: F 168 GLU cc_start: 0.9088 (mp0) cc_final: 0.8685 (pm20) REVERT: F 175 LEU cc_start: 0.9452 (mp) cc_final: 0.9068 (mp) REVERT: F 179 MET cc_start: 0.8712 (ptt) cc_final: 0.8489 (ptm) REVERT: F 216 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8552 (t0) REVERT: F 254 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8486 (tm-30) REVERT: F 258 TYR cc_start: 0.8480 (t80) cc_final: 0.8064 (t80) REVERT: F 330 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8908 (pp) REVERT: F 385 MET cc_start: 0.9149 (ttm) cc_final: 0.8771 (ttp) REVERT: F 480 ARG cc_start: 0.9311 (mtm110) cc_final: 0.9083 (mtm-85) REVERT: F 505 SER cc_start: 0.9069 (t) cc_final: 0.8607 (p) REVERT: N 1 MET cc_start: 0.5821 (OUTLIER) cc_final: 0.2758 (pp-130) REVERT: G 37 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8083 (mm) REVERT: G 51 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8798 (pp) REVERT: G 70 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8389 (mtp) REVERT: G 98 GLU cc_start: 0.9198 (mp0) cc_final: 0.8898 (mp0) REVERT: G 124 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8793 (tppt) REVERT: G 136 ARG cc_start: 0.8908 (ttm110) cc_final: 0.8536 (mtp-110) REVERT: G 150 MET cc_start: 0.8520 (tmm) cc_final: 0.8002 (tmm) REVERT: G 168 GLU cc_start: 0.9008 (mp0) cc_final: 0.8628 (pm20) REVERT: G 224 ARG cc_start: 0.8686 (ttt90) cc_final: 0.8359 (ttt90) REVERT: G 254 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8495 (tm-30) REVERT: G 258 TYR cc_start: 0.8718 (t80) cc_final: 0.8415 (t80) REVERT: G 272 VAL cc_start: 0.8792 (t) cc_final: 0.8414 (p) REVERT: G 330 ILE cc_start: 0.9479 (OUTLIER) cc_final: 0.9078 (pp) REVERT: G 352 GLU cc_start: 0.9231 (tm-30) cc_final: 0.8750 (tm-30) REVERT: G 393 THR cc_start: 0.8550 (p) cc_final: 0.8205 (p) REVERT: G 469 GLN cc_start: 0.9279 (tm-30) cc_final: 0.8654 (tt0) REVERT: O 1 MET cc_start: 0.5887 (OUTLIER) cc_final: 0.4926 (pmm) REVERT: H 37 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7994 (mm) REVERT: H 70 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8427 (mtp) REVERT: H 75 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8074 (mm-30) REVERT: H 128 ARG cc_start: 0.8996 (mmm-85) cc_final: 0.8619 (mmm160) REVERT: H 136 ARG cc_start: 0.8947 (ttm110) cc_final: 0.8594 (mtp-110) REVERT: H 150 MET cc_start: 0.8440 (tmm) cc_final: 0.7894 (tmm) REVERT: H 168 GLU cc_start: 0.9117 (mp0) cc_final: 0.8700 (pm20) REVERT: H 175 LEU cc_start: 0.9501 (mp) cc_final: 0.9238 (mp) REVERT: H 206 LYS cc_start: 0.8368 (mmmt) cc_final: 0.7999 (mmmt) REVERT: H 216 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8622 (t0) REVERT: H 330 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8864 (pp) REVERT: H 352 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8690 (tm-30) REVERT: H 385 MET cc_start: 0.9099 (ttm) cc_final: 0.8634 (ttp) REVERT: H 386 MET cc_start: 0.8998 (mtm) cc_final: 0.8741 (mtp) REVERT: H 393 THR cc_start: 0.8443 (p) cc_final: 0.8080 (p) REVERT: H 395 GLU cc_start: 0.8747 (mp0) cc_final: 0.8477 (mp0) REVERT: P 1 MET cc_start: 0.6124 (OUTLIER) cc_final: 0.3151 (pp-130) outliers start: 221 outliers final: 159 residues processed: 1030 average time/residue: 0.1791 time to fit residues: 304.4536 Evaluate side-chains 1122 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 918 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 309 GLN Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain P residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 260 optimal weight: 2.9990 chunk 157 optimal weight: 0.0170 chunk 200 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 220 optimal weight: 0.0060 chunk 22 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 overall best weight: 0.4234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.138656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.104082 restraints weight = 51371.192| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.53 r_work: 0.3062 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32360 Z= 0.121 Angle : 0.717 12.400 43936 Z= 0.336 Chirality : 0.047 0.206 5000 Planarity : 0.003 0.032 5456 Dihedral : 14.602 168.317 4710 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 6.20 % Allowed : 27.54 % Favored : 66.26 % 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: -1.13 (0.13), residues: 3968 helix: 0.13 (0.14), residues: 1296 sheet: -1.44 (0.22), residues: 520 loop : -1.08 (0.14), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 105 TYR 0.011 0.001 TYR H 353 PHE 0.012 0.001 PHE A 401 HIS 0.005 0.000 HIS F 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (32352) covalent geometry : angle 0.71650 / 0.34 (43936) hydrogen bonds : bond 0.03018 / 2.00 ( 992) hydrogen bonds : angle 4.94391 / 3.36 ( 2832) Misc. bond : bond 0.00020 / 0.01 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 974 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8057 (mm) REVERT: A 51 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8671 (pp) REVERT: A 70 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.7253 (mpp) REVERT: A 124 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8731 (tppt) REVERT: A 128 ARG cc_start: 0.8583 (mtp-110) cc_final: 0.8303 (mtm110) REVERT: A 136 ARG cc_start: 0.8972 (ttm110) cc_final: 0.8615 (mtp-110) REVERT: A 150 MET cc_start: 0.8415 (tmm) cc_final: 0.7833 (tmm) REVERT: A 168 GLU cc_start: 0.9011 (mp0) cc_final: 0.8561 (pm20) REVERT: A 216 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8646 (t0) REVERT: A 224 ARG cc_start: 0.8587 (ttt90) cc_final: 0.8165 (ttt90) REVERT: A 272 VAL cc_start: 0.8697 (t) cc_final: 0.8378 (p) REVERT: A 330 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.8888 (pp) REVERT: A 337 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8152 (tp) REVERT: A 352 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8738 (tm-30) REVERT: A 385 MET cc_start: 0.9085 (ttm) cc_final: 0.8831 (ttp) REVERT: A 393 THR cc_start: 0.8417 (p) cc_final: 0.8123 (p) REVERT: A 411 TYR cc_start: 0.8882 (t80) cc_final: 0.8187 (t80) REVERT: A 469 GLN cc_start: 0.9229 (tm-30) cc_final: 0.8632 (tt0) REVERT: I 1 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.3228 (pp-130) REVERT: B 37 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7787 (mm) REVERT: B 51 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8792 (pp) REVERT: B 75 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8057 (mm-30) REVERT: B 128 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.7044 (mpp-170) REVERT: B 168 GLU cc_start: 0.9074 (mp0) cc_final: 0.8793 (pm20) REVERT: B 206 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7901 (mmmm) REVERT: B 216 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8371 (t0) REVERT: B 232 ASP cc_start: 0.8901 (m-30) cc_final: 0.8380 (t0) REVERT: B 258 TYR cc_start: 0.8401 (t80) cc_final: 0.8062 (t80) REVERT: B 272 VAL cc_start: 0.8699 (t) cc_final: 0.8356 (p) REVERT: B 330 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.8933 (pp) REVERT: B 393 THR cc_start: 0.8512 (p) cc_final: 0.8291 (p) REVERT: B 469 GLN cc_start: 0.9263 (tm-30) cc_final: 0.9046 (tt0) REVERT: C 37 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8016 (mm) REVERT: C 51 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9056 (pp) REVERT: C 70 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.7618 (mpp) REVERT: C 75 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8033 (mm-30) REVERT: C 136 ARG cc_start: 0.8864 (ttm110) cc_final: 0.8519 (mtp-110) REVERT: C 168 GLU cc_start: 0.8959 (mp0) cc_final: 0.8698 (pm20) REVERT: C 175 LEU cc_start: 0.9406 (mp) cc_final: 0.9139 (mp) REVERT: C 216 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8465 (t0) REVERT: C 254 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8399 (tm-30) REVERT: C 272 VAL cc_start: 0.8831 (t) cc_final: 0.8477 (p) REVERT: C 330 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.9016 (pp) REVERT: C 337 LEU cc_start: 0.8574 (mp) cc_final: 0.8369 (mp) REVERT: C 385 MET cc_start: 0.9153 (ttm) cc_final: 0.8751 (ttp) REVERT: C 469 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8995 (tt0) REVERT: C 480 ARG cc_start: 0.9251 (mtm110) cc_final: 0.9030 (mtm-85) REVERT: C 512 ARG cc_start: 0.8456 (mtp180) cc_final: 0.7949 (mmm160) REVERT: K 1 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.3032 (pp-130) REVERT: D 37 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7877 (mm) REVERT: D 51 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8578 (pp) REVERT: D 70 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.7689 (mpp) REVERT: D 112 GLN cc_start: 0.8724 (mm110) cc_final: 0.7905 (mp10) REVERT: D 136 ARG cc_start: 0.8897 (ttm110) cc_final: 0.8544 (mtp-110) REVERT: D 150 MET cc_start: 0.8243 (tmm) cc_final: 0.7653 (tmm) REVERT: D 168 GLU cc_start: 0.9094 (mp0) cc_final: 0.8818 (pm20) REVERT: D 175 LEU cc_start: 0.9535 (mp) cc_final: 0.9305 (mp) REVERT: D 330 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8878 (pp) REVERT: D 385 MET cc_start: 0.9139 (ttm) cc_final: 0.8765 (ttp) REVERT: D 395 GLU cc_start: 0.8845 (mp0) cc_final: 0.8472 (mp0) REVERT: D 469 GLN cc_start: 0.9336 (tm-30) cc_final: 0.8794 (tt0) REVERT: D 480 ARG cc_start: 0.9307 (mtm110) cc_final: 0.9066 (mtm-85) REVERT: L 1 MET cc_start: 0.5703 (OUTLIER) cc_final: 0.3154 (pp-130) REVERT: E 16 ASP cc_start: 0.8405 (t0) cc_final: 0.8106 (t0) REVERT: E 37 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8144 (mm) REVERT: E 51 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8743 (pp) REVERT: E 70 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.7260 (mpp) REVERT: E 128 ARG cc_start: 0.8688 (mmm-85) cc_final: 0.8367 (mmm160) REVERT: E 136 ARG cc_start: 0.8876 (ttm110) cc_final: 0.8542 (mtp-110) REVERT: E 168 GLU cc_start: 0.9063 (mp0) cc_final: 0.8653 (pm20) REVERT: E 175 LEU cc_start: 0.9247 (mp) cc_final: 0.9015 (mp) REVERT: E 224 ARG cc_start: 0.8578 (ttt90) cc_final: 0.8111 (ttt90) REVERT: E 254 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8518 (tm-30) REVERT: E 258 TYR cc_start: 0.8575 (t80) cc_final: 0.8258 (t80) REVERT: E 265 GLN cc_start: 0.8783 (mp10) cc_final: 0.8567 (mt0) REVERT: E 272 VAL cc_start: 0.8836 (t) cc_final: 0.8564 (p) REVERT: E 330 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.9048 (pp) REVERT: E 352 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8764 (tm-30) REVERT: E 385 MET cc_start: 0.9098 (ttm) cc_final: 0.8664 (ttp) REVERT: E 411 TYR cc_start: 0.8876 (t80) cc_final: 0.8316 (t80) REVERT: E 465 GLN cc_start: 0.8461 (pt0) cc_final: 0.8092 (mt0) REVERT: E 469 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8956 (tt0) REVERT: F 37 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8067 (mm) REVERT: F 70 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.7304 (mpp) REVERT: F 136 ARG cc_start: 0.8870 (ttm110) cc_final: 0.8519 (mtp-110) REVERT: F 150 MET cc_start: 0.8355 (tmm) cc_final: 0.7811 (tmm) REVERT: F 168 GLU cc_start: 0.9078 (mp0) cc_final: 0.8759 (pm20) REVERT: F 175 LEU cc_start: 0.9442 (mp) cc_final: 0.9164 (mp) REVERT: F 216 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8389 (t0) REVERT: F 258 TYR cc_start: 0.8584 (t80) cc_final: 0.8260 (t80) REVERT: F 312 ASN cc_start: 0.9283 (t0) cc_final: 0.8835 (t0) REVERT: F 330 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8806 (pp) REVERT: F 385 MET cc_start: 0.9096 (ttm) cc_final: 0.8702 (ttp) REVERT: F 411 TYR cc_start: 0.8836 (t80) cc_final: 0.8304 (t80) REVERT: F 469 GLN cc_start: 0.9300 (tm-30) cc_final: 0.8699 (tt0) REVERT: F 480 ARG cc_start: 0.9278 (mtm110) cc_final: 0.9066 (mtm-85) REVERT: F 505 SER cc_start: 0.9092 (t) cc_final: 0.8707 (p) REVERT: N 1 MET cc_start: 0.6055 (OUTLIER) cc_final: 0.3017 (pp-130) REVERT: G 37 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8034 (mm) REVERT: G 51 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8730 (pp) REVERT: G 98 GLU cc_start: 0.9193 (mp0) cc_final: 0.8838 (mp0) REVERT: G 136 ARG cc_start: 0.8893 (ttm110) cc_final: 0.8525 (mtp-110) REVERT: G 150 MET cc_start: 0.8543 (tmm) cc_final: 0.8016 (tmm) REVERT: G 168 GLU cc_start: 0.9022 (mp0) cc_final: 0.8698 (pm20) REVERT: G 216 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8415 (t0) REVERT: G 224 ARG cc_start: 0.8606 (ttt90) cc_final: 0.8132 (ttt90) REVERT: G 254 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8474 (tm-30) REVERT: G 258 TYR cc_start: 0.8763 (t80) cc_final: 0.8063 (t80) REVERT: G 272 VAL cc_start: 0.8648 (t) cc_final: 0.8225 (p) REVERT: G 330 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9089 (pp) REVERT: G 352 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8727 (tm-30) REVERT: G 393 THR cc_start: 0.8343 (p) cc_final: 0.8055 (p) REVERT: G 411 TYR cc_start: 0.8890 (t80) cc_final: 0.8458 (t80) REVERT: G 469 GLN cc_start: 0.9272 (tm-30) cc_final: 0.8747 (tt0) REVERT: O 1 MET cc_start: 0.5789 (OUTLIER) cc_final: 0.4910 (pmm) REVERT: H 37 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7951 (mm) REVERT: H 51 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8514 (pp) REVERT: H 70 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.7347 (mpp) REVERT: H 128 ARG cc_start: 0.8977 (mmm-85) cc_final: 0.8620 (mmm160) REVERT: H 136 ARG cc_start: 0.8920 (ttm110) cc_final: 0.8565 (mtp-110) REVERT: H 150 MET cc_start: 0.8413 (tmm) cc_final: 0.7854 (tmm) REVERT: H 168 GLU cc_start: 0.9135 (mp0) cc_final: 0.8718 (pm20) REVERT: H 175 LEU cc_start: 0.9493 (mp) cc_final: 0.9259 (mp) REVERT: H 206 LYS cc_start: 0.8378 (mmmt) cc_final: 0.7917 (mmmt) REVERT: H 216 ASP cc_start: 0.9041 (OUTLIER) cc_final: 0.8506 (t0) REVERT: H 330 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8731 (pp) REVERT: H 352 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8624 (tm-30) REVERT: H 385 MET cc_start: 0.9019 (ttm) cc_final: 0.8617 (ttp) REVERT: H 386 MET cc_start: 0.8846 (mtm) cc_final: 0.8539 (mtp) REVERT: H 393 THR cc_start: 0.8352 (p) cc_final: 0.7536 (t) REVERT: H 395 GLU cc_start: 0.8777 (mp0) cc_final: 0.8301 (mp0) REVERT: H 411 TYR cc_start: 0.8769 (t80) cc_final: 0.8295 (t80) REVERT: H 469 GLN cc_start: 0.9268 (tm-30) cc_final: 0.8657 (tt0) REVERT: P 1 MET cc_start: 0.6020 (OUTLIER) cc_final: 0.3093 (pp-130) outliers start: 203 outliers final: 128 residues processed: 1049 average time/residue: 0.1795 time to fit residues: 311.0039 Evaluate side-chains 1102 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 931 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 309 GLN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain P residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 109 optimal weight: 0.8980 chunk 279 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 262 optimal weight: 0.0970 chunk 155 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 258 optimal weight: 3.9990 chunk 286 optimal weight: 0.0470 chunk 57 optimal weight: 0.9990 chunk 346 optimal weight: 4.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 HIS ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.139018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.104392 restraints weight = 51514.975| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.55 r_work: 0.3069 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 32360 Z= 0.126 Angle : 0.723 12.455 43936 Z= 0.339 Chirality : 0.048 0.214 5000 Planarity : 0.003 0.032 5456 Dihedral : 14.337 169.088 4710 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.78 % Allowed : 28.39 % Favored : 65.83 % 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: -1.10 (0.14), residues: 3968 helix: 0.13 (0.14), residues: 1296 sheet: -1.49 (0.23), residues: 504 loop : -1.04 (0.14), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 105 TYR 0.022 0.001 TYR A 258 PHE 0.012 0.001 PHE B 165 HIS 0.004 0.000 HIS F 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (32352) covalent geometry : angle 0.72344 / 0.34 (43936) hydrogen bonds : bond 0.03026 / 2.00 ( 992) hydrogen bonds : angle 4.89471 / 3.32 ( 2832) Misc. bond : bond 0.00025 / 0.01 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8075.69 seconds wall clock time: 139 minutes 19.49 seconds (8359.49 seconds total)